DATA & INFORMATION WEB SITES
 

Information Web Site	URL Location
Jefferson County MRC	http://mrc.co.jefferson.wa.us
UW Fisheries Research Institute	http://www.fish.washington.edu/Publications/frireps.html
NOAA Regional Library	http://www.wrclib.noaa.gov/lib/
Washington Dept. Fish and Wildlife-Homepage	http://www.wa.gov/wdfw/
WDFW - Forage Fish	http://www.wa.gov/wdfw/fish/forage/forage.htm
NOAA Northwest Fisheries Science Center	http://research.nwfsc.noaa.gov/pubs/nwfscpubs.html
National Marine Mammal Laboratory	http://www.nmfs.noaa.gov/prot_res/PR2/Stock_Assessment_Program/sars.html
Department of Ecology-Publications Page	http://www.ecy.wa.gov/pubs.html
Dept. of Ecology Water Quality Data	http://www.ecy.wa.gov/programs/eap/mar_wat/mwm_intr.html
Dept. of Ecology-Environmental Assessment Bibliography	http://www.wa.gov/programs/eap/biblio/index.html
Puget Sound Health 2000 PSWQAT	http://www.wa.gov/puget_sound/Publications/pshealth2000/index.html
Wa. Dept. of Health Shellfish PSP Hotline	http://www.doh.wa.gov/ehp/sf/biotox.htm
UW Library	http://catalog.lib.washington.edu/search~/

There is ample evidence that marine resources of the Northwest Straits are in serious decline. Bottom fish, forage fish, salmon, sea birds, invertebrates, and some populations of marine mammals have declined precipitously since 1980. The Jefferson County Marine Resources committee is a citizen-based effort to identify regional marine issues, foster community understanding and involvement, recommend positive action, and develop support for various protection and restoration measures.

This annotated bibliography is a product of the Jefferson County Marine Resources 2000 literature review and data search on the status of marine resources in Jefferson County. Information was collected from an extensive review of existing literature. This included existing literature reviews, peer reviewed literature, agency reports, and a search of electronic databases for all documents pertaining to marine resources in Jefferson County with a particular focus on that region of Jefferson County that falls within the boundaries of the Northwest Straits Commission. Those marine waters bounded by the Hood Canal Bridge, San Juan County, Island County, and Clallam County is the primary area of focus.

This search included interviews with leading experts and resource managers on specific species and ecosystem components and included, but was not limited to, a search of the following electronic databases: Aquatic Sciences and Fisheries Abstracts (ASFA), UW Fisheries Research Institute Reports, the National Technical Information Service (NTIS), and the University of Washington library database. The University of Washington Library, UW Fisheries Research Institute Reports, and NTIS electronic databases have unlimited internet access. The ASFA database has limited on-line membership access but is available on compact disk in the University of Washington, Fisheries and Oceanography library. The ASFA database includes literature dating back to 1982 covering science, technology, and management of marine and freshwater environments. It includes 5,000 international sources in the form of primary journals, source documents, books, monographic series, conference proceedings and technical research reports. The University of Washington library catalog has unlimited internet access at http://catalog.lib.washington.edu/search~/. Numerous agency reports and the UW School of Fisheries, Fisheries Research Institute Reports (UW-FRI) database which includes over 500 reports pertaining to research conducted by the Fisheries Research Institute (FRI) personnel from 1973 to the present are also available on the internet. In addition to the above literature and data search, information has been collected through interviews with leading experts and resource managers. Through this process, we have assembled a comprehensive collection of literature and information regarding the status of marine resources in Jefferson County. In addition to this annotated bibliography, the products of this data search process include: a Jefferson County MRC on-line bibliography available on the MRC web site at http://mrc.co.jefferson.wa.us, a summary report, and an enhanced literature collection for the Jefferson County MRC physical library that is available to MRC members and interested members of the general public.
 
 

Keywords: marine birds//marine mammals//Puget Sound//northwest straits//straits

Abstract: Characteristic mammals, birds, fishes, invertebrates and plants are presented for different marine habitats in Puget Sound.

Antrim, L. D., R. M. Thom, W. W. Gardiner, V. I. Cullinan, D. K. Shreffler and R. W. Bienert. Effects of petroleum products on bull kelp (Nereocystis luetkeana). Marine Biology. 1995. 122:23-31.

Keywords: kelp//water quality//nearshore vegetation//vegetation//nearshore

Abstract: Although research has been conducted on the effects of oil on the giant kelp Macrocystis pyrifera, no similar studies have been completed on bull kelp, Nereocystis leutkeana, the dominant kelp in Washington State, British Columbia, and Alaska. The effects of three petroleum products [diesel fuel, intermediate fuel oil (IFO) and crude oil] were tested before and after weathering on N. leutkeana. Whole plants were exposed to petroleum product for 4 or 24 h and then transferred to the field. Observations on the condition of the plants were made daily for 7 d. In addition, controlled bioassays were performed to measure the effects of petroleum exposure on net photosynthetic rate (NP) and respiration rate, using light and dark-bottle techniques. These experiments verified the susceptibility of N. leutkeana tissue to the damaging effects of direct exposure to several oil types. The 4 h exposures to weathered diesel and unweathered IFO, and 24 h exposures to unweathered and weathered diesel and IFO resulted in moderate to severe damage to kelp tissue (i.e. resulted in moderate to severe damage to kelp tissue (i.e. clearly delineated bleached line accompanied by tissue necrosis). Weathered diesel was more toxic than unweathered diesel. The most severe damage to bull kelp was concentrated at the meristematic zone (junction of stipe and bulb) where new tissue growth occurs. Petroleum type significantly affected stipe and blade NP, R and NP:R ratios. Diesel treatments had a greater negative effect on NP than did the IFO treatments. Based on these experiments, the relative ranking of the damaging effects of petroleum treatment on bull kelp ware weathered diesel>unweathered IFO>unweathered diesel>weathered IFO>unweathered crude>weathered crude.

Armstrong, J. W. and A. E. Copping. Status and Management of Puget Sound's Biological Resources. Conference Proceedings No. EPA 910/9-90-001Seattle, WA. EPA. 1990.

Keywords: marine resources// marine biology//wildlife management//fishery management//Puget Sound

Abstract: A collection of papers presented to the Forum on the Status and Trends of Puget Sound’s Biological Resources: How well are we managing Puget Sound’s Biological Resources, Commercial and recreational management of aquatic vegetation in Puget Sound, geoducks, commercial geoduck dive fishery, management of nongame marine iInvertebrates, Puget Sound crab and shrimp management, management of the commercial dive fisheries for sea urchins and sea cucumbers, intertidal fisheries for hardshell clams and oyster, Puget Sound tribal fisheries management-a cooperative approach, status of anadromous game fish in Puget Sound, Hood Canal salmon, marine fish users and managers, cooperative management of marine birds in Washington, cooperative management of Puget Sound waterfowl resources, management of Washington marine mammals under the Marine Mammal Protection Act, paradox or opportunity and priorities in managing Puget Sounds’ species.

Bargmann, G. C. Schmitt, W. Palsson, S. Hoffman, G. Lippert, and G. Davis. Management approaches for recreational fisheries for bottomfishing Puget Sound. WDFW. 1991. Washington Department of Fisheries Progress Report No. 288.

Keywords: fish//bottomfish//groundfish//cod//rockfish//lingcod//pollock//halibut
Abstract: WDFW is developing bottomfish management plans that incorporate angler and diver preferences with the goal to conserve fish resources. This report presents three general approaches for managing recreational fisheries for bottomfish in Puget Sound. These approaches represent various trade-offs between management simplicity and attainable harvest. Information about existing recreational fisheries for bottomfish, fish biology, and angler preferences, as well as expectations of increased fishing effort, are reviewed and analyzed in the development of a recommended management approach.

Bargmann, G. G. The biology and fisheries for lingcod (Ophiodon elongatus) in Puget Sound. WA. 1982. Wash. Dept. Fish. Tech. Rep. No. 66.

Keywords: Puget Sound//lingcod//fish

Abstract: Seasonal and annual harvest trends for lingcod are analyzed for the inland marine waters of Washington. Age analysis and length information resulted in year class strength trends, age at recruitment, growth, and yield.

Bargmann, G.G. Studies on Pacific Cod in Agate Pass, Washington. 1980. Wash. Dept. Fish. Prog. Rep. 123.

Keywords: fish//cod//bottomfish//groundfish//Puget Sound

WDF investigated the sport fishery for Pacific cod (Gadus macrocephalus) in Agate Pass, WA. Between December 20, 1976 and April 10, 1977. It is estimated that 3,840 angler trips harvests 12,200 fish, calculated at 39,200 pounds total weight. The mean length was 50.3 cm females significantly the larger fish, and males outnumbering females in the catch. During the study, fish were tagged and recoveries indicated that the Pacific tomcod were moving rapidly through the pass in a generally southerly direction, diminishing the effect of the fisheries on a particular group of stock. Tag returns during the following year (1979) indicated a dispersion of the cod throughout Puget Sound and included one tag returned form coastal waters. The Pacific cod fishery is more widespread than when last studied, with sport efforts considerably enlarged.

Beamish, R. J. Protecting Plants and Animals in the Strait of Georgia: Ideas for Action by the Work Group on the Protection of Marine Plants and Animals in the Strait of Georgia. Draft.

Keywords: Northwest Straits//straits//nearshore//fish//northwest

Abstract: This report presents the set of action plans the Puget Sound/Georgia Basin International Task Force finalized in response to the 1994 Marine Science Panel recommendations. The Task Force divided into Work Groups. This is the report form the Protection of Marine Plants and Animals Work Group. In response to Immediate Policy Concerns, the Work Group proposed the following actions: integrate and coordinate governing bodies and agencies responsible for the health of the Strait of Georgia ecosystem; create MPAs; prevent loss of nearshore and estuarine habitat; preserve biodiversity; develop new management methods; involve the public; establish a code of conduct on the environment; control pollution and toxic discharges into the Strait of Georgia; assess current policies and management activities in the Strait of Georgia, and take global warming seriously. In response to the loss of foreshore and estuarine areas, they identified the need to take action to: not divide management at the tideline; reduce urban and industrial pollution; prevent introduction of exotic species; exchange information; improve assessment of marine mammal abundance; preserve juvenile salmon rearing capacity; establish an ongoing program to assess the health of all species in the Strait of Georgia, and communicate scientific and government information to the public.

A state of the strait is presented along with a series of papers on creating a sustainable future, share marine waters, fisheries sustainability, and contaminants in the Strait of Georgia and elsewhere. A series of papers and studies are summarized in this report.

Bernthal, Carol,T. Labbe, and B. Rot. Hood Canal/Eastern Strait of Juan de Fuca Summer Chum Habitat Recovery Plan. Final Draft. 1999.

Keywords: Hood Canal// Puget Sound//Jefferson County//salmon//summer chum//Hood Canal Summer Chum/ salmon recovery//fish habitat//salmon habitat

Abstract: This is a preliminary assessment for identifying the limiting factors and establishing criteria for the development of a recovery plan for the Hood Canal summer chum who became listed as" threatened" in 1999, under the Endangered Species Act. The final version of this document is an implementation plan for summer chum recovery. It is the April 2000 Summer Chum Salmon Conservation Initiative.

Berry, Helen and B. Ritter. Puget Sound Intertidal Habitat Inventory 1995: Vegetation and Shoreline Characteristics. Olympia, WA: Washington State Department of Natural Resources (DNR); 1995.

Keywords: nearshore//nearshore vegetation//inventory//shorelines//habitat

Abstract: Summary of DNR intertidal habitat survey of 110 miles of shoreline in Whatcom and                  Skagit Counties in the DNR Nearshore Habitat Program as part of the Puget Sound Ambient Monitoring     Program (PSAMP). Survey identified vegetation type and shoreline characteristics.

Berry, Helen T. F. Mumford G. C. Schoch M. N. Dethier. Mapping Shorelines in Puget Sound III: Management Applications for Inventory and Monitoring. In: Proceedings of Puget Sound Research '98 Conference. March 12-13, 1998. Seattle, WA. Olympia, WA. DNR.

Keywords: nearshore//vegetation//Puget Sound//straits

Abstract: Nearshore habitat degradation and loss are recognized to be major threats to the health of Puget Sound (British Columbia/Washington Marine Science Panel, 1994). Inventory data is needed to characterize the quantity, location, and quality of habitats, and to guide land use planning. Information on trends in habitat health is needed to identify the habitat features and functions that are most at risk, and to relate these changes to the state of the Puget Sound ecosystem. The Nearshore Habitat component of the Puget Sound Ambient Monitoring Program (PSAMP) has the dual goals of inventorying nearshore habitat and monitoring trends in health. For the purpose of the monitoring program, nearshore habitat includes the physical and biotic components of intertidal and shallow subtidal areas. Monitoring habitat is a challenge due to the size and complexity of the study area, which includes approximately 2,400 miles of shoreline east of Cape Flattery, and encompasses a wide range of habitats, from vertical rocky shores to wide, protected mudflats. Human activities range from intensive, in the highly industrial urban embayments, to relatively minor in the least developed areas.

Bertolotto, Chrys. The citizen shoreline inventory. Puget Sound Research '98. 1998 Mar 13-1998 Mar 14. Seattle, WA. Olympia, WA. PSWQAT.

Keywords: shoreline//Puget Sound//habitat

Abstract: This paper reports on a new inventory program uniting the need to fill information gaps on Puget Sound shoreline habitat conditions and provide education and training opportunities for the community as to the value of shorelines and the anthropogenic impacts to those nearshore habitats. The findings of this inventory is available on internet as a Citizen Shoreline Atlas.

Boersma, P. D. and J. K. Parrish. Limiting abuse: marine protected areas, a limited solution. Special Issue: Ecological Economics and Sustainable Governance of the Oceans.Ecological-Economics. 1999. Vol. 31(no. 2): 287-304.

Keywords: marine protected areas//MPA

Abstract: Designation of marine protected areas (MPAs) is increasing as humans seek to combat over-exploitation of marine resources and preserve the integrity of the ocean's unique biodiversity. At present, there are over 1300 MPAs. The primary legal responsibility for the designation of MPAs falls to individual countries, but protection of the marine environment at large scales is also critical because ocean circulation does not honor legal boundaries and often exceeds the influence of any one nation or group of nations. There are many reasons for establishing MPAs. The papers surveyed principally referred to scientific, economic, cultural, and ethical factors. Two approaches predominated: fisheries management and habitat protection. Although the major threat to terrestrial systems is habitat loss, the major threats to the world's oceans are fisheries overexploitation, coastal development, and chemical and biological pollution. MPAs may provide conservation of formerly exploited species as well as benefits to the fishery through leakage of 'surplus' adults (spillover) and larvae (larval replenishment) across reserve boundaries. Higher order effects, such as changes in species richness or changes in community structure and function, have only been superficially explored. Because many MPAs are along coastlines, within shipping lanes, and near human centers of activity, the chance of chemical and biological pollution is high. Use of MPAs to combat development and pollution is not appropriate, because MPAs do not have functional boundaries. The ocean is a living matrix carrying organisms as well as particles and therefore even relatively environmentally sensitive uses of coastal ecosystems can degrade ecosystem structure and function via increasing service demands (e.g. nutrient and toxics transformation) and visitation. Whether an MPA is effective is a function of the initial objectives.

Bradbury, Alex B. Sizemore D. Rothaus and M. Ulrich. Stock Assessment of Subtidal Geoduck Clams (Panopea abrupta) in Washington. Washington Department of Fish and Wildlife Fish Program, Fish Management Division, Marine Resources Unit. 2000 Jan. Report Number: FPT00-01

Keywords: Geoduck//clams//invertebrates//shellfish

Abstract: This report presents commercial tract densities and average weights. Biomass estimate calculations are presented and a model for an age-based equilibrium yield to predict long-term consequences of various harvest rates, using estimated geoduck life history parameters. The model predicts yield and spawning biomass per recruit over a range of fishing mortality rates. A strategy is recommended as a risk-averse policy for geoducks.

British Columbia/Washington Marine Science Panel. The shared marine waters of British Columbia and Washington. British Columbia/Olympia, WA. 1994.

Keywords: marine birds//fish//salmon//birds//invertebrates//water quality//shellfish//MPA//marine protected areas//Puget Sound//northwest straits//marine mammals//nearshore//human impacts//contaminants//straits

Abstract: Nearshore habitat degradation and loss are recognized to be major threats to the health of Puget Sound (British Columbia/Washington Marine Science Panel, 1994). Inventory data is needed to characterize the quantity, location, and quality of habitats, and to guide land use planning. Information on trends in habitat health are needed to identify the habitat features and functions that are most at risk, and to relate these changes to the state of the Puget Sound ecosystem.

The Nearshore Habitat component of the Puget Sound Ambient Monitoring Program (PSAMP) is responsible for inventorying nearshore habitat and monitoring trends in health. For the purpose of the monitoring program, nearshore habitat includes the physical and biotic components of intertidal and shallow subtidal areas. Monitoring habitat is a challenge due to the size and complexity of the study area, which includes approximately 2,400 miles of shoreline east of Cape Flattery, and encompasses a wide range of habitats, from vertical rocky shores to wide, protected mudflats. Human activities range from intensive in the highly industrial urban embayments to relatively minor in the least developed areas.

The Nearshore Habitat Program inventories nearshore vegetation through the collection and classification of multispectral sensor collected shoreline data field surveys in conjunction with photo interpretation. At current funding levels, sound-wide mapping will be completed within 15-20 years. A PSAMP review in 1995 recommended examining alternative methods to map resources soundwide in less than five years (Shen, 1995). Additionally, it recommended initiating a program to monitor trends in nearshore habitat health. This paper responds to the recommendations. It reviews user needs, how current systems fulfill user needs, and how inventory methods are being changed in response. It then reviews results of research which testing the feasibility of using a linked geophysical mapping and biologic sampling model for inventory and monitoring known as SCALE (Shoreline Classification and Landscape Extrapolation).

Broadhurst, Ginny and R. Wlakinshaw. Puget Sound nearshore habitat regulatory perspective: A review of issues and obstacles. Olympia, WA: Puget Sound Water Quality Action Team. 1998 (Puget Sound/Georgia Basin Environmental Report Series: Number 7).

Keywords: nearshore habitat//regulatory framework//permits//vegetation/ docks// piers//runoff//shoreline armoring//growth management act//endangered species act//regulations//shorelines

Abstract: This report characterizes nearshore habitat losses and provides an overview of those regulatory mechanisms in place addressing causes of habitat losses. It identifies current regulatory gaps relevant to the protection of nearshore habitat and reviews the extent of nearshore habitat modifications throughout the Puget Sound and straits region. It discusses industrial and residential impacts to habitats and provides present regulatory structure and a brief regulatory analysis of the framework, agency roles, and gaps in the current regulatory system.

Buckley, R. M. and G. J. Hueckel. The influence of prey communities on fish species assemblages on artificial reefs in Puget Sound, Washington. Envinron-Biol. Fish.1987. Vol. 19(no. 3): pp. 195-214.

Keywords: Puget Sound//fish//artificial reef

Abstract: Research on eleven artificial reefs in Puget Sound, Washington examined the relative importance of reef-produced prey items to recreationally important reef fish species assemblages. The colonization of potential prey items, and fish species assemblages to ten artificial reefs were examined for the reefs first two to five years, and observations were conducted on an eleventh reef during its forty-ninth productive year.

Buckley, Raymond M. Substrate associated recruitment of juvenile Sebastes in artificial reef and natural habitats in Puget Sound and the San Juan Archipelago, Washington. Olympia, WA: Washington Dept. of Fish and Wildlife, Fish Management Program, Resource Assessment Division; 1997.

Keywords: rockfish//juvenile rockfish//rockfish recruitment//Puget Sound//San Juan Islands

Abstract: Habitat pathways and temporal and spatial parameters of substrate- associated recruitment have never been reported for juvenile quillback rockfish (S.maliger) in any ecosystem, and have never been described for juvenile copper (S. caurinus) and splitnose (S. diploproa) rockfish in Washington waters. In 1991-1994, juvenile quillback rockfish recruited only during July-August each cohort-year, correcting biannual recruitment errors in the literature for Puget Sound; first recruitment was apparently to offshore benthic habitats, with subsequent migrations to nearshore benthic macrophytes. Copper rockfish recruited during July-September each cohort-year; first recruitment was to surface and shallow water macrophytes attached to benthic substrates, with subsequent migrations to benthic macrophytes. During November-January, juvenile quillback and copper rockfish in natural macrophyte habitats migrated offshore associated with benthic drift macrophytes; juveniles in artificial and natural reef habitats migrated to deeper water associated with crevices in the substrates. Juvenile splitnose rockfish recruited during June-August each cohort-year; first recruitment was to surface drift macrophyte and seagrass habitats, which were vacated by December. Apparently co-occurring pelagic juvenile copper and splitnose rockfish selectively recruited to attached and detached vegetation habitats respectively.

Development of internal micro-tagging procedures for juvenile Sebastes enabled the first estimation of instantaneous natural loss rate (mortality and emigration) for this genus, without non-immigration assumptions. The estimate of Z258d=0. .0106 for quillback rockfish on an artificial reef recruitment habitat was lower than for a coastal pelagic species, the only other estimate for juveniles Sebastes. Nearshore artificial reef substrate manipulations functioned as juvenile rockfish recruitment habitats, providing preferred nursery and refuge habitats and enhancing local recruitment. Efficacies of artificial reef recruitment habitats located adjacent to, and isolated from, established reefs, were affected by variability in levels of juvenile rockfish recruitment, biogenic habitat parameters, and ecological maturity of the substrates. Micro-tagged juvenile rockfishes remained on artificial reef recruitment habitats during the cohort-year contrasting emigrations form natural macrophyte habitats during the cohort-year contrasting emigrations from natural macrophyte habitats. Increased densities of juvenile rockfish on artificial reef recruitment habitats late in the cohort-year indicated emigrations form natural habitats. Juvenile rockfish had average daily growth rates of 0.11-0.13 mm total length in both natural and artificial reef recruitment habitats.

Calambokidis, J. Contaminants in Puget Sound Marine Mammals: Temporal, Spatial, and Species-Related Patterns. Puget Sound Research '95. January 12-14. Bellevue, WA. Olympia, WA. PSWQA. 1995. pp. 901-908.

Keywords: marine mammals//contaminants//water quality//human impacts

Abstract: This paper reviews principal studies conducted on contaminants in Puget Sound marine mammals and examines the patterns in concentrations of chlorinated hydrocarbons among species, across locations, and over time. Harbor Seals: PCB concentrations in blubber were found to be 50 to 100 times higher than the concentration in their prey reflecting the high proportion of contaminants they were absorbing from their prey and their limited ability to excrete or metabolize such compounds. Concentrations of PCBs and DDT were significantly higher in pups collected in southern Puget Sound than those from the Strait of Juan de Fuca. However concentrations of metals and trace elements showed no significant difference by site. Lead and silver were significantly higher in seals from the Strait of Juan de Fuca than from southern Puget Sound. Killer Whales: Concentrations of PCBs in blubber ranged form 0.9 to 250 ppm and total DDTs from 1.7 to 250 ppm and total DDTs from 1.7 to 640ppm. Spatial and temporal trends were not apparent. Unlike harbor seals, levels of DDT in killer whales were higher than PCBs. This was interpreted as indicating these animals were found to either primarily feeding outside of the greater Puget Sound region, a region predominating in PCBs, or their prey came from outside this region. For the Harbor porpoise, distinct differences in concentrations of contaminants were found among regions with a consistent increase in DDT concentrations along the coast of the Southern California Bight. PCBs in blubber ranged from under 1 ppm in an animal recovered on the Washington coast to 55 ppm in an animal from southern Puget Sound.Gray Whales: Concentrations of chlorinated hydrocarbons were low, PCBs in blubber ranged from 0.01 to 3 ppm. No significant differences were found by region. Concentrations of PCB's and DDT were lowest in minke whales and pygmy sperm whales. Much higher concentrations of PCBs and DDT were found in Dall's porpoise and river otters.

These studies reveal important patterns. The impacts of contaminants to harbor seals and killer whales demonstrate these two species to have the highest exposure to contaminants. Monitoring of contaminant trends and patterns in harbor seals are recommended due to existing data demonstrating clear regional and temporal patterns in contamination.

Calambokidis, J. and J. Quan. Gray whales in Washington State: Report on research in 1996. Final report to National Marine Mammal Laboratory, Seattle, WA. 1997.

Keywords: mammals//marine mammals//whales//gray whales

Abstract: This report summarizes research conducted by Cascadia Research in collaboration with the National Marine Mammal Laboratory during the 1996 field season. Cascadia Research has been conducting research on gray whales in Washington waters using photographic identification of individual animals since the mid-1980s (Calambokidis et al. 1994) with the goals of determining the number of whales using Washington waters, preferred areas for feeding, seasonality of use, and degree to which animals return year to year. Fifty boat surveys were conducted by biologists with Cascadia to observe gray whales between 15 March and 6 October 1996 totaling 243 hours of observation and 1,486 nmi of coverage. These included dedicated boats surveys conducted using a rigid-hulled inflatable and effort aboard whalewatch trips. The heaviest effort was in Grays Harbor, the western the Strait of Juan de Fuca, the northernWashington outer coast, and in the northern Puget Sound area. Data were also contributed by biologists at the National Marine Mammal Laboratory who provided identification photographs of gray whales made on an additional 13 days (between 13 June and 26 September) from surveys on the northern outer coast and the western Strait of Juan de Fuca. Gray whales were individually identified using photographs of the natural markings on the right and left sides. Comparisons of identified individuals were made to Cascadia’s catalog of over 100 gray whales seen in previous years off Washington as well as catalogs of identification photographs taken by collaborating researchers in British Columbia. In 1996, Cascadia Research and the Whale Museum received a total 112 gray whale sighting reports. were received by Cascadia Research and the Whale Museum in 1996. A total of 47 different gray whales were identified. A high proportion of the whales identified in three regions (northern Washington coast, Strait of Juan de Fuca, and southern Vancouver Island) were seen multiple times (73-79% by region) and had been identified in a previous year (64-82%). Gray whales identified near Grays Harbor early in the season were less likely to have been seen multiple times (52%) or a previous year (26%). Because most of these whales were identified in the migratory corridor during the migration (26-52%) when we would expect to be seeing migratory whales, this lower proportion of ‘resident’ whales was surprisingly high. Gray whales were frequently identified in multiple regions indicating movement patterns. Comparison of photographic catalogs with researchers working in British Columbia revealed that many of the whales that feed along the Washington coast through the summer range along the British Columbia coast to areas north of Vancouver Island. Conclusions of the research conducted through 1996 include: Gray whale use of southern and central Puget Sound is highly variable; few animals came into these waters in 1996. Previous research has shown whales that have been identified in these waters have never been resighted across years and have not been seen in other regions. A consistent group of individual gray whales had returned annually to the waters around Whidbey Island but the duration of their stay has become shorter. In 1996 we were not successful in finding these animals in this or any other region. A consistent group of individual whales feed each summer along the Washington outer coast and Strait of Juan de Fuca and range north past Vancouver Island. Some of these animals have returned over a 20-year period.

Calambokidis, J. and R. W. Baird. Status of marine mammals in the Strait of Georgia, Puget Sound, and Juan de Fuca Strait and potential human impacts. pp. 282-303 In: Review of the marine environment and biota of Strait of Georgia, Puget Sound, and Juan de Fuca Strait. [(R.C.H. Wilson, R.J. Beamish, F. Aitkens, and J. Bell, Ed.). Canadian Technical Report of Fisheries and Aquatic Sciences No. 1948.]. Proceedings of the BC/Washington Symposium on the Marine Environment, 1994 Jan 13.

Keywords: marine mammals//Puget Sound

Abstract: Nine species of marine mammals commonly occupy the trans-boundary waters of British Columbia and Washington (BC/WA). Animals of all species move across this international border. Of the four pinniped species common to these waters, harbour seals are the most numerous and the only one that breeds in these waters. Approximately 30,000 harbour seals occur in the trans-boundary area. Harbour seal populations have increased at 10-15% per year. The numbers of California sea lions and elephant seals have also been increasing steadily although neither breeds in BC/WA waters. Steller sea lions, a species that is declining through most of its range, also occur in this region. Of the five cetacean species common to the waters, harbour and Dall's porpoise are the most abundant and number in the several thousands. Harbour porpoise numbers in some areas have declined since the 1940s, though little data are available to assess current trends in populations of these two species. Killer whales are the best studied marine mammal species in the area, with most of the individuals in the populations that use these waters identified photographically. Over 20,000 gray whales migrate past the entrance to the Strait of Juan de Fuca and some individuals spend prolonged periods feeding in the spring and summer in BC/WA waters. A small number of minke whales also return annually to these waters to feed during the spring, summer, and fall. Marine mammals are vulnerable to human activities in the BC/WA trans-boundary waters. High concentrations of contaminants, especially chlorinated hydrocarbons and some metals, have been identified in these animals. Highest concentrations of contaminants have been found in harbour seals (from southern Puget Sound) and killer whales. Determination of the impacts of these contaminants on marine mammals in these waters has been inconclusive, though in other areas contaminant exposure has caused reproductive failure and immunosuppression. Marine mammals are killed incidental to commercial fishing operations, particularly harbour porpoise, Dall's porpoise, and harbour seals. Information to assess human impacts on most marine mammals and to adequately evaluate their current status is extremely limited.

Calambokidis, J., G. H. Steiger, B. D. McLaughlin, and J. R. Evenson. Harbor seal haul-out habitat and the feasibility of shifting haul-out locations at Dosewallips State Park, Washington. Report to the Washington State Parks and Recreation Commission. Olympia, Washington. 1990.

Keywords: seals//marine mammals//Washington//Jefferson County

Abstract: High fecal coliform concentrations found at the Dosewallips River delta on the Hood Canal appear to originate from harbor seals that use the sloughs and marsh on the southern portion of the delta to haul out (Calambokidis et al. 1989, Calambokidis and McLaughlin 1988, DSHS 1988). In other areas in Puget Sound, harbor seals regularly haul out on human-made platforms, such as recreational floats and log booms (Calambokidis et al. 1978, 1985, Johnson and Jeffries 1977). Harbor seals used to haul-out on a log boom that existed at the north end of the Dosewallips River Delta through the mid 1970s. Because seal-related contamination is closely associated with haul-out locations, it may be possible to alter the affected areas by shifting the areas used by seals to haul out. This study examines the feasibility of shifting the seal haul-out habitat at Dosewallips delta from the salt marsh areas used currently to human-made structures that would be located just off the delta. We summarize relevant findings about the biology of harbor seals at this location, harbor seal haul-out requirements, what steps would need to be taken to shift the location of haul-out, and limitations of trying to conduct such a project. Counts made on 49 days from December 1989 to August 1990 at Dosewallips Delta ranged from 11 to 390 harbor seals and averaged 140 (n=49, s.d.=85). A number of factors were identified that were statistically associated with the variations in the number of seals counted at the Dosewallips Delta. These included time of day, temperature, and tide height and time to high tide. A major surprise from the results of this study was the significant decline in seal numbers at the Dosewallips River Delta in recent years. This trend data should be viewed with caution, especially because it does not cover some critical seasons. There were not significant increases or decreases in seal numbers observed at Duckabush River Delta or Quilcene Bay. At the Dosewallips River delta, harbor seals haul out along the three main southern sloughs and along or on logs along the river. We found significant seasonal and annual changes in the use of different portions of the Dosewallips River Delta. A trial float placed at Dosewallips River delta in May 1990 was showed no seal use until June 1990 and no regular use until late July. Females with pups were shown to occasionally haul-out on the float in late August towards the end of the pupping season. Exploratory behavior by seals in the water of the trial float was seen frequently. The amount of haul-out space required per seal was similar among locations and habitats and averaged about 2 m2/seal. The area used by seals at human-made habitats tended to be slightly larger than natural habitats, though this difference was small. The mean shoreline distance per seal (the distance of shoreline or water access for a group of seals) was generally under 1 m/seal at natural habitats and greater than

1 m/seal at human-made habitat. Human-made haul-out areas appear to provide some advantages over natural habitats, especially in their accessibility at all tides and their rapid access to deep water. The height above water for human-made structures used by seals, including log booms, floats, and a fish net pen, ranged from 12 to 54 cm with log booms lowest in the water. Float height above the water appeared to prevent newborn seal pups from getting out on the float for the first 1-2 weeks. It was calculated that a haul-out structure to accommodate the maximum number of seals observed to use the current haul-out area (470) would need to be 1,175 m2 using 2.5 m2 per seal. Shoreline space would need to be at least 1 m per seal or about 500 m total. This is less of a limiting factor since the haul-out area designs discussed below and human-made haul-out areas in general, easily meet this requirement. Human-made structures, log booms and floats, represent the best choices for alternate habitat at Dosewallips and a combination of both structures would provide the best alternative habitat for harbor seals. To allow segregation between groups we recommend use of multiple small structures as opposed to one or two large structures. The ideal log-boom structure consists of three logs secured together by crosspieces with total width of 1.5 m. For the float design, the most suitable and compact structure would be a series of open-celled concrete floats. A fairly compact 12 x 17m structure would be suitable for up to 60 harbor seals. A marked barrier around the structures would be necessary to keep boaters away from hauled seals and restrict them from using the structures for recreational purposes. The best location for an alternate haul-out site is along the steep slope marking the edge of the delta just north of the main river channel. Seals may not readily adapt to new structures.

Calambokidis, J., J. L. Laake, and S. D. Osmek. Aerial surveys for marine mammals in Washington and British Columbia inside waters. Final report to the National Marine Mammal Laboratory, Seattle, WA. 1997.

Keywords: marine mammals//san juans//straits

Abstract: Aerial line-transect surveys were conducted during August 1996 primarily to estimate harbor and Dall’s porpoise abundance in five regions, encompassing US and Canadian waters of the Strait of Juan de Fuca, San Juan/Gulf Islands, and Strait of Georgia. A total of 6,263 km of on-transect effort were completed using a twin-engine high-wing aircraft flying at 90 knots and an altitude of 600 feet. Three observers searched for marine mammals through side bubble windows and a downward viewing port. Out of 1,505 groups sighted (3,340 animals) while on-effort, 1,074 were harbor seals, 311 were harbor porpoise, and 76 were Dall’s porpoise. We estimate abundance of harbor porpoise and Dall’s porpoise using line-transect methods. A re-analysis of aerial surveys conducted in 1991 was also completed to provide a comparable dataset using similar regional boundaries and analysis methods to look at temporal trends.

Calambokidis, J. J., R. Evenson, G. H. Steiger, and S. J. Jeffries. Gray whales of Washington State: natural history and photographic catalog.Olympia, WA. Cascadia Research Collective. 1994.

Keywords: whales//marine mammals

Abstract: This report provides a description of population status, migratory movements, feeding habits, sighting reports, behavior and feeding, and mortality statistics for gray whales in Washington State.

Calambokidis, J. J., R. Evenson, J. C. Cubbage, S. D. Osmek, D. Rugh, and J. L. Laake. Calibration of sighting rates of harbor porpoise from aerial surveys. Report to the National Marine Mammal Laboratory, National Marine Fisheries Service. Seattle, WA.1993.

Keywords: porpoise//marine mammals

Abstract: Harbor porpoise abundance estimates have been made for Washington and Oregon using aerial and vessel surveys (Barlow 1988, Barlow et al. 1988, Calambokidis In Press, Calambokidis et al. 1991, 1992, Green et al. 1992 Turnock et al. In press). A major limitation of these estimates, however, has been that the fraction of animals missed on the survey line was not known. The primary objective of this study was to experimentally determine a correction factor for harbor porpoise missed during aerial surveys. Two methods were used to evaluate the correction factor for animals missed. The primary method for obtaining a correction factor was to measure the sighting success by aerial observers of specific harbor porpoise groups being tracked from land. Harbor porpoise groups in the study area were tracked from land prior to the aircraft passes. Secondarily, we gathered breath rate data on harbor porpoise groups to determine the proportion of time they are at the surface and likely to be seen by aerial observers. This was similar to the method used by Barlow et al. (1988) in devising a correction factor. The calibration experiment was conducted off the northwest side of Orcas Island in the San Juan Islands, Washington. Aerial surveys with a twin-engine aircraft were conducted in conjunction with land observations on 7 days between 3 August and 13 August 1992. A total of 547 transect lines were flown in 33 flight hours completing approximately 26 hours of transect surveys. Two teams, each consisting of 4-6 people made observations of harbor porpoise from land. Each team used an electronic theodolite interfaced with a computer data acquisition system. Radio contact between one of the aircraft personnel and the land teams was used to select aircraft transects that would include passing over a harbor porpoise group being tracked from land. To determine the proportion of harbor porpoise groups seen from the aircraft, several criteria were used to select the harbor porpoise groups that would be used for the calibration and to determine whether a group tracked from land was seen by the aerial observers. Harbor porpoise groups were included as a sample in the calibration only if: 1) they were seen from land within 4 minutes of the passage of the aircraft, and 2) were within 100m of the aircraft transect line. A harbor porpoise group being tracked from land was considered seen by the aerial observers if the position of the porpoise determined from land and air was less than 300m and if the number of porpoises in the group determined from the air was not more than twice or less than half the size determined from land. Using the parameters described above, 28 of 92 (30.4%) harbor porpoise groups within 100m of the transect line were seen by the aerial observers and 69.6% were missed. The point estimate for g(0) (the probability of sighting a group that was on the transect line) was 0.324 (SE=0.056). The sample size for this estimate was better than expected and provides a low enough variance that it will be able to be applied without greatly increasing the overall variance of abundance estimates. The correction factor for animals missed on the transect line was almost identical to that determined previously by Barlow et al. (1988) based on breath rate data of harbor porpoise. Seven different harbor porpoise groups whose surfacing were monitored spent an average of 36 sec (sd= 13.1) at or near the surface and 120 sec (sd=31.0) on longer dives of 30 sec or more. These values likely underestimate the time groups spend at the surface because some surfacings may have been missed. The proportion of harbor porpoise at the surface (potentially visible from the air) based on breath rates was slightly lower than the proportion seen in the calibration experiment. This may have been a result of our underestimating the time porpoise are at the surface (due to missing some surfacings). This also suggests that relatively few harbor porpoise on the transect line that were at the surface when the aircraft flew over were missed during the calibration experiment. The proportion of time we calculated harbor porpoise were at the surface from the breath rate data was similar to that reported by Barlow et al. (1988).

Calambokidis, J. S., J. Jeffries, P. S. Ross, and M. Ikonomou. Temporal trends in contaminants in Puget Sound harbor seals. Final Report to U.S. EPA and Puget Sound Water Quality Action Team. Olympia, WA. Cascadia Research. 1999.

Keywords: marine mammals//Puget Sound//contaminants//seals

Abstract: Harbor seals (Phoca vitulina) are the most abundant marine mammal species in Washington State and occur throughout the marine waters including Puget Sound. Extremely high concentrations of some chlorinated hydrocarbon contaminants, especially PCBs, were found in Puget Sound harbor seals in the 1970s and 1980s. One of the longest-term datasets on trends in contaminants in the Puget Sound region comes from harbor seal studies. Harbor seal pups from Puget Sound have been collected or biopsied for testing concentrations of PCBs and DDT compounds at 4-5 year intervals from 1972 to 1997 at several Puget Sound sites including Gertrude Island in southern Gertrude Island in southern Puget Sound and Smith Island in the Strait of Juan de Fuca. Samples from harbor seals are ideally suited for trend analyses because they are highly contaminated, represent an integration of concentrations in a broad selection of prey in a region, and, with the utilization of non-emaciated pups, provide limited inter-sample variability allowing sensitive detection of changes over time. The most recent analyses were of both dead harbor seal neonates collected in 1996 and 1997 and biopsy samples of blubber from weaned harbor seal pups collected in 1993 and 1996 at Gertrude Island. We determined current levels of a broad range of chlorinated hydrocarbon contaminants in Puget Sound harbor seals including congener-specific concentrations of PCBs, DDTs and other pesticides, and the first analyses of polychlorinated dibenzo dioxins and furans (PCDDs and PCDFs). We tested both the most recent samples and re-tested some of the historical samples from 1984 and 1990 to provide more detailed data on historical contaminants. Harbor seals have proven to be an excellent indicator of environmental contamination at the upper level of the food chain with clear spatial and temporal differences detected. While concentrations of PCBs and DDT have declined dramatically since the 1970s, concentrations have stabilized since the mid-1980s with only slight declines since then. Even though concentrations have declined, harbor seals are clearly still at risk, with the current concentrations of PCBs and the TEQ in pups within the range identified as causing immunotoxicity in seals. Most of the TEQ came from PCBs rather than PCDDs or PCDFs. The plan is to continue monitoring trends in harbor seal contamination in Puget Sound at regular intervals and update trend data from other sites in Washington State.

Calambokidis, J., S. M. Speich, J. Peard, G. H. Steiger, J. C. Cubbage, D. M. Fry, and L. J. Lowenstine. Biology of Puget Sound marine mammals and marine birds: Population health and evidence of pollution effects. NOAA Tech. Memo. NOS OMA 18, National Technical Information Service. Springfield, VA. 1985.

Keywords: contamination//Puget Sound//birds//marine mammals

Abstract: The objective of this research was to determine whether detrimental effects possibly caused by toxic chemicals could be observed in Puget Sound marine mammals and marine birds. The study design was based on examination of a wide variety of indices of population and individual health and comparison of these indices from areas of suspected high contaminant levels (target areas) to those from areas of suspected low contaminant levels (reference areas) and to those reported by other researchers. Recent research conducted in Puget Sound has revealed high levels of contaminants in fish, marine mammals, and marine birds. High contaminant levels in Puget Sound have been correlated to abnormalities and disorders in fish. Researchers have also reported possible linkages between contaminants and disorders in marine mammals and marine birds in other parts of the world. Primary species considered here are harbor seal, Glaucous-winged Gull, Great Blue Heron, and Pigeon Guillemot; these species were chosen because they reside, feed, and breed in some of the most contaminated portions of Puget Sound. Three other mammal species (killer whale, harbor porpoise, and river otter) were chosen as secondary study species either because they seasonally occur in contaminated areas of Puget Sound or they were found through previous research to be experiencing problems that might be pollutant-related. Target areas were chosen that were as close as possible to the heavily contaminated Elliott and Commencement Bays. Reference areas used for different species included sites north of Puget Sound, in the Hood Canal, and in Grays Harbor and Willapa Bay on the Washington outer coast. Several biological parameters were examined to evaluate the evidence for pollutant-related problems. These parameters included population distribution, population trends, measures of reproductive success, mortality, causes of death, incidence of gross and histological pathology, and incidence of physical deformities or disorders seen in the population. To detect a broad range of possible effects, both general population health as well as incidence of individual disorders previously linked to contaminants were examined and measured. Study methods varied by species. Censuses were made from the ground, boats, and from small aircraft and provided population figures for several species. Reproductive rates were determined from censuses and for birds, by observing marked nests. Mortality and the incidence of reproductive disorders were determined from breeding area searches and censuses made during the breeding season. Gross pathology was determined from necropsies of animals found dead and for some species from collected individuals. Samples for histopathology, microbiology, blood parameters, and eggshell thickness were collected from appropriate species and examined by specialists for comparison between locations. Tissues for contaminant analysis were collected and archived, but not analyzed. We found a wide variety of disorders in some marine mammal and marine bird species. Some of these disorders followed patterns consistent with known patterns of contaminant concentrations in Puget Sound. Evidence for possible pollutant-related disorders is summarized. Overall, populations of the study species are doing very well, with the exception of the harbor porpoise and the killer whale; these two populations have declined in the Puget Sound area. For harbor porpoise the decline occurred prior to the 1970s and for killer whales the evidence of a decline is recent. Harbor seal numbers are generally increasing in all our study areas, however, an unusually high incidence of premature births and neonatal mortality was found at some sites. These disorders are similar to those that have been linked to effects of contaminants in pinnipeds from other parts of the world. The high incidence of these disorders seen in Puget Sound seals, however, was found not at sites with suspected high contaminant levels but, rather unexpectedly, at study sites with suspected low contaminant levels. The most likely explanation for these problems is disease agents in these populations compounded by the possibility that these areas are nearing carrying capacity for seal numbers. A significantly higher incidence of disorders and umbilical lesions found in contaminated areas reflects a pattern of impacts associated with contaminant presence. Puget Sound marine bird populations do not appear to be declining or experiencing major reproductive problems. Two of three primary study species (Glaucous-winged Gull and Great Blue Heron), however, did show significant eggshell thinning compared to pre-1947 measurements. In addition, Pigeon Guillemots had lower overall eggshell thickness than those reported for pre-1947, but the difference was not statistically significant. These findings suggest a possible persistent detrimental effect of the pesticide DDT (and its primary metabolite, DDE) as has been reported for a wide variety of bird species in other areas. We also found evidence of highly variable liver weights in gulls that may have been associated with contaminants. No conclusive statements regarding the association between contaminants and eggshell thinning or liver weights can be made until chemical analyses of archived tissues are conducted. Contaminant analysis of archived samples would greatly augment this study in several ways. This analysis is important in order to: verify assumptions about contaminant exposure of different populations; provide a better comparison with findings in other areas; allow correlation tests between disorders found in specific animals and their contaminant burdens, and describe trends in recent contaminant exposure of marine mammals and marine birds.

Calambokidis, J. and Baird, R. W. Status of marine mammals in the Strait of Georgia, Puget Sound and the Juan de Fuca Strait and potential human impacts [Review of the Marine Environment and Biota of Strait of Georgia, Puget Sound and Juan de Fuca Strait Proceedings of the BC/Washington Symposium of the Marine Environment] Wilson, R. C. H.; Beamish, R. J., Aitkens, F., and Bell, J. (eds). BC/Washington Symp. on the Marine Environment, Vancouver, BC (Canada), 13-14 Jan 1994. Sidney, BC Canada. Institute-of-Ocean-Sciences. 1994: pp. 283-303.

Keywords: marine mammals//straits

Abstract: In this report the authors summarize what is known about the status of marine mammals that occur in the transboundary area, examine potential human impacts on marine mammals, and make research recommendations.

Calambokidis, J., S.M. Speich, J. Peard, G.H. Steiger and J.C. Cubbage. Biology of Puget Sound marine mammals and marine birds: Population health and evidence of pollution effects. Office of Oceanography and Marine and Assessment. Rockville, MD. National Ocean Serv. NOAA TECH. MEMO. 1985. NTIS Order No.: PB91-172734/GAR. NOAA/TM/NOS/CMA-18 (NOAATMNOSCMA18).

Keywords: birds//marine mammals//Puget Sound

Abstract: The objective of the research was to determine whether detrimental effects possibly caused by toxic chemicals could be observed in Puget Sound marine mammals and marine birds. The study design was based on examination of a wide variety of indices of population and individual health and comparison of these indices from areas of suspected high contaminant levels (target areas) to those from areas of suspected low contaminant levels (reference areas) and to those reported by other researchers. Primary species considered here are harbor seal. Glaucous-winged Gull, Great Blue Heron, and Pigeon Guillemot; these species were chosen because they reside, feed, and breed in some of the most contaminated portions of Puget Sound. Three other mammal species (killer whale, harbor porpoise, and river otter) were chosen as secondary study species either because they seasonally occur in contaminated areas of Puget Sound or they were found through previous research to be experiencing problems that might be pollutant-related. (DBO).

Calambokidis, J., Steiger, G. H., Lowenstine, L. J., and Becker, D. S. Chemical contamination of harbor seal pups in Puget Sound Puget Sound. Puget Sound Estuary Program. Bellevue, WA: PTI Environmental Services; 1991. NTIS Order. PB92-132778/GAR.

Keywords: marine mammals//Puget Sound//contaminants//water quality//seals

Abstract: Dead newborn harbor seals (Phoca vitulina) were collected from Smith Island in the Strait of Juan de Fuca and from Gertrude Island in southern Puget Sound. A variety of chemical contaminants were measured in different kinds of tissue from seven harbor seal pups from each location. Various tissues were also evaluated microscopically for histopathological abnormalities. Two methods for determining the concentrations of PCBs and DDE in blubber tissues were compared. Concentrations of PCBs, lead and silver were significantly higher in the seals from Gertrude Island than those from Smith Island. However, the concentrations of PCBs in seal pups from both locations have declined significantly since testing began in 1972.

Canning, Dougals J. and H. Shipman (Shoreland and Environmental Assistance Program). Coastal erosion management studies in Puget Sound, Washington: Executive Summary. Olympia, WA. Washington Department of Ecology 1996 Jan. Report 94-74. Coastal Erosion Management Strategy; Coastal Erosion Management Studies, Vol. 1.

Keywords: geology//coastal erosion/erosion management

Abstract: This report is an executive summary of reports by Department of Ecology Coastal Erosion management Studies contractors. It does not address commercial and industrial land uses. The study area covers Puget Sound from Olympia north to the Canadian border. The report describes Puget Sound geology, shoreline stabilization techniques, the extent of shoreline armoring in Thurston County, management of coastal erosion and shoreline stability, erosion management techniques, and impacts to biological resources and ecological systems along with institutional approaches and policy tools.

Cardwell, Rick D. and C. E. Woelke. Water Quality Compendium for Washington State. Washington State Department of Fisheries; 1979. Grant No. R80503210. (II. Data).

Keywords: water quality//Port Townsend

Abstract: Contains results of biomonitoring studies of Port Townsend with a majority of over thirty sampling stations located adjacent to the paper mill discharge pipe. One site south of Protection Island near diamond Point, two off of downtown Port Townsend, and one mid-basin in Discovery Bay.

Casillas, E. M., R. Arkoosh, E. Clemons, T. Hom, D. Misitano, T. K. Collier, J. E. Stein, and U. Varanasi. Chemical contaminant exposure and physiological effects in outmigrant juvenile chinook salmon from urban estuaries of Puget Sound, Washington. In: Puget Sound Research '95. 1995. Jan 12-14 1995. Bellevue, WA. Olympia, WA. 1995. pp. 657-665.

Keywords: water quality//salmon//Puget Sound//fish//contaminants

Abstract: Overview of data collected from studies over the period of 1989 to 1993 on the effects of chemical contaminant exposure on juvenile chinook salmon in polluted urban Puget Sound estuaries. The data collected reveals increased exposure of juvenile chinook salmon to toxic chemicals in these estuaries. Juvenile salmon inhabiting contaminated urban estuaries displayed immune system alterations and impaired growth when compared to juveniles from hatcheries or non-urban estuaries. Juveniles from the Duwamish Waterway showed immunosuppression and increased disease susceptibility to Vibrio anguillarum. Studies during this period provide evidence of linkage between juvenile chinook salmon health and elevated contaminant levels in polluted estuaries.

Center for Marine Conservation, Marine Resources. A Citizens Guide to Marine Resources of the Northwest Straits.1998.

Keywords: MPA//fish//marine birds//marine mammals//salmon//herring//rockfish//cod//nearshore//oil spills//water quality//impacts//shellfish//invertebrates//northwest straits//straits//nearshore

Abstract: A guide providing citizen access to information on the status and health of marine resources in the region of the Northwest Straits. It includes resource maps and information on invertebrates, marine fish, salmon, seals and sea lions, marine birds and marine mammals of the Northwest Straits and human impacts on habitats in the Northwest Straits.

Cohen, Andrew, C. Mills, H. Berry, M. Wonham, B. Bingham, B. Bookheim, J. Carlton, J. Chapman, J. Cordell, L. Harris, T. Klinger, A. Kohn, C. Larbert, G. Lambert, K. Li, D. Secord, and J. Toft. A Rapid Assessment Survey of Non-indigenous Species in the Shallow Waters of Puget Sound. Lacey, WA. Washington State Department of National Resources. 1998 Puget Sound, Hood Canal, Strait of Georgia and adjoining waters.

Keywords: non-indigenous species//invertebrates/Puget Sound//shellfish

Abstract: This report presents the results of a sampling expedition of 32 sampling stations in Puget Sound and the San Juan area from southern most sites like Shelton and Mud Bay, central Puget Sound, Port Ludlow, Port Hadlock, Port Townsend, Port Orchard, Seabeck, Brownsville from Steilacoom to Blaine along the mainland, Friday Harbor, Argyle Lagoon, Anacortes, Samish River, Swinomish Cannel, Cornet Bay, Bellingham, and Blaine. This rapid assessment for non-indigenous marine organisms focused primarily on non-quantitative or semi-quantitative sampling of dock fouling organisms growing on floating docks.

Cox, Jack K. McDonald and T. Rigert. Engineering and Geotechnical Techniques for Shoreline Erosion Management in Puget Sound. Olympia, WA. Washington State Department of Ecology.1994.Report 94-77. Coastal Erosion Management Studies. Vol. 4. Shorelands and Environmental Assist. Program.

Keywords: erosion//shoreline

Abstract: Reports on technically feasible shoreline protection techniques including soft solutions using natural site features and materials, composite systems combining hard and soft solutions, building setbacks and drain field removal. Erosion processes are described including identification of an erosion problem, techniques for erosion control and a site-specific decision model to help landowners and regulators select solutions.

Cross, J. N., K. Fresh, B. S. Miller, C. A. Simenstad, S. N. Steinfort, and J. C. Fegley. Nearshore fish and macroinvertebrate assemblages along the Strait of Juan de Fuca including food habits of the common nearshore fish. Seattle, WA: UW, School of Fisheries, Fisheries Research Institute. 1978. FRI-UW-7818.

Keywords: fish//bottomfish//rockfish//cod//groundfish

Abstract: This reports on a baseline study to document the distribution, abundance, and biomass of nearshore fishes along the Strait of Juan de Fuca, to determine their food habits, and to identify the macroinvertebrates collected incidentally with the fish. A total of 93 species of fish was collected from 1976 to 1978. Trends in occurrence, abundance, and biomass for individual species were fairly consistent between 1976-77 and 1977-78. The predominant nearshore demersal fish species in beach seine collections were the Pacific staghorn sculpin, Eng. sole, and sand sole. The dominant neritic fish species in townet collections were the Pacific herring and longfin smelt. The predominant intertidal fish species were the northern clingfish, tidepool sculpin, and high cockscomb. Species richness generally increased from west to east in beach seines and townet collections while the opposite trend was observed in tidepool collections. Species richness and density was highest in summer and fall and lowest in winter. 53 of 55 common nearshore resident species preyed upon gammarid amphipods. Gammarids composed more than 50% of the total Index of Relative Important for 31 fish species and than 75% for 9 species. Calanoid copepods were the dominant prey of neritic fishes.

Deriso, R. B., T. J. Quinn II, and P. R. Neal. Catch at age analysis with auxiliary information. Can. J. Fish. Aquat. Sci. 42:815-824. 1985.

Keywords: harvest//fish

Abstract: The authors review techniques for estimating the abundance of migratory populations and develop a new technique based on catch-age data from geographic regions and their earlier technique, catch-age analysis with auxiliary information. Data requirements are catch-age data over several years, some auxiliary information, and migration rates among regions. The model, containing parameters for year-class abundance, age selectivity, full-recruitment fishing mortality, and catchability, is fitted to data with a nonlinear least squares algorithm. A measurement error model and a process error model are presented and favor the process error model because all model parameters can be jointly estimated. By application to data on Pacific halibut, Hippoglossus stenolepis, the process error model converges readily and produces estimates with no significant bias.

Determan, Tim. 1999 Status and trends in fecal coliform pollution in Puget Sound embayments. 2000 Washington State Dept. of Health and Office of Food Safety and Shellfish Program.

Keywords: shellfish//pollution//port townsend//kilisut//fecal coliform//

Abstract: This report is a Department of Health (DOH) summary of fecal coliform pollution in 45 Puget Sound shellfish areas from January 1998-March 1999. It reports the status, trends and discusses sources. Jefferson County sites include Protection Island, Discovery Bay, Kilisut Harbor, Port Townsend Bay, and Dosewallips State Park. Dosewallips River delta was the only site in Jefferson County showing fecal coliform pollution in one or more stations. Maps of sites are provided.

Dethier, M. A Marine and Estuarine Habitat Classification System for Washington State. Washington Natural Heritage Program.Olympia, WA. Washington State Department of Natural Resources. 1990.

Keywords: vegetation//habitat//vegetated habitat//nearshore

Abstract: Stresses on marine ecosystems due to changing global climate and the encroachment of human development are manifested in the Pacific Northwest by loss of habitat and the reduction or extinction of many important organisms. Studying the ecological functions of marine habitats and measuring the extent and rate of habitat loss is important to determining the health of Puget Sound. To monitor habitat changes in Puget Sound, there is a need to map shoreline types and inventory the marine biota for: 1) measuring change due to natural or human-caused perturbations; 2) mapping areas with key resources or potential for these, and 3) choosing sites for research and for monitoring programs. Our ability to detect changing the biota of the Sound requires that the information we gather about the biota has a sufficiently fine spatial scale of resolution, and that we take steps to minimize the inherent variability that exists in all ecological data sets. One way to do both is to take into account the geophysical features of the shorelines being mapped or studied as such features strongly affect biotic communities.

Doty, D. C. R. M. Buckley and J. E. West. Identification and protection of nursery habitats for juvenile rockfish in Puget Sound, Washington. Puget Sound Research '95 Proceedings; Bellevue, WA. Olympia, WA. 1995. pp.181-190.

Keywords: rockfish//Puget Sound

Abstract: Summary of a study identifying nursery habitats for three demersal Puget Sound rockfish species. Recruitment was concentrated along the northwestern shoreline of central Puget Sound. Young-of-the-year (YOY) rockfish were found to use all three kelp, macroalgae, and eelgrass vegetated habitat types with kelp habitat supporting the highest densities. The vegetated habitats appeared to provide refuge for juveniles making the transition from pelagic to benthic habitats. The findings suggest that vegetated habitats may be necessary for replenishing and maintaining adult populations of copper, quillback, and brown rockfish. Recommendations include using vegetated habitats for juvenile rockfish as a habitat management. The study supports the use of vegetated habitats to be considered in habitat management and mitigation. Most recruitment of YOY rockfish in this study occurred in urbanized shorelines where habitat degradation and alteration were common. Such shoreline changes and habitat degradation may effect natural rockfish production. This study data is now incorporated into Washington Administrative Code (WAC).

Keywords: non-indigenous species//Puget Sound//straits

Abstract: This report was commissioned by the Puget Sound Water Quality Authority through an agreement between the U.S. Environmental Protection Agency (EPA) and the Canadian Department of Fisheries and Oceans (DFO). Its purpose is to assist the Washington and British Columbia Working Groups on Minimizing the Introduction of Exotic Species in developing recommendations to the British Columbia Washington Environmental Cooperation Council. It assesses the status and management of NIS introductions into the shared marine waters of British Columbia and Washington. Pathways of NIS introduction are evaluated, and the management programs in place to reduce risks from these pathways are described. It is intended that from this report and from the work groups that will consider it, recommendations will emerge that address risk and management of NIS introductions, and needs for further information.

Pathways of NIS introduction to the shared marine waters include aquaculture activities; the aquarium trade; public aquaria; releases of NIS by individuals; commercial, military, and recreational marine vessels; research institutions; and seafood commodity distribution. Risk of NIS introduction from aquaculture is well defined, the industry is highly regulated, and active processes are underway for continuous review of aquaculture activities as they involve NIS. Risk of NIS introduction from aquarium activities and release of NIS by individuals is poorly defined, and only limited information is available to define the risks from research, seafood distribution, and marine recreational vessel activities. The relative risk associated with the large inoculation of marine NIS from ballast water discharges is assessed from shipping industry data and relevant scientific literature. Management of NIS in other selected states and countries is briefly reviewed.

Engel, J. and R. Kvitek. Effects of otter trawling on a benthic community in Monterey Bay National Marine Sanctuary. Conservation Biology. 1998. 12:1204-1214.

Keywords: MPA//marine protected areas//commercial harvest//harvest//commercial fishery//trawl

Abstract: Bottom trawling is one of the most disruptive and widespread human-induced physical disturbances to seabed communities and has become a global environmental concern. We used a comparative approach to test the hypothesis that persistent otter trawling decreases bottom habitat complexity and biodiversity, increases the abundance of opportunistic species, and benefits prey important in the diet of some commercially valuable fish. We compared two similar and adjacent fishing areas at 180 m off central California in Monterey Bay National Marine Sanctuary: one inside the three-mile coastal zone of restricted fishing with light levels of trawling and one beyond the three-mile limit with high levels of trawling. Differences in fishing effort between the two areas were confirmed and quantified by means of data and tow number statistics from Pacific Fishery Management Council (PFMC) Trawl Logbook records. We used still photography, video footage, bottom grab samples, and experimental trawling to compare the physical and biological parameters of the two areas. The area with high levels of trawling had significantly more trawl tracks, exposed sediment, and shell fragments and significantly fewer rocks and mounds and less flocculent material than the lightly trawled area. Most invertebrate epifauna counted were significantly more abundant in the lightly trawled area. Densities of the polychaetes, Chloeia pinnata, as well as that of oligochaetes, ophiuroids, and nematodes were higher every year in the highly trawled area, and there were significantly fewer polychaete species every year in the highly trawled area. Content analysis of fish guts showed that C. pinnata was a dominant prey item for some of the commercially important flatfishes in both lightly and heavily trawled areas. Our study provides evidence that high levels of trawling can decrease bottom habitat complexity and biodiversity and enhance the abundance of opportunistic species and certain prey important in the diet of some commercially important fishes. This work also illustrates how constraints currently imposed on fisheries research by the near universal absence of true unfished control sites severely limit our ability to determine appropriate levels of harvest pressure for maintaining sustainable fisheries and marine biodiversity. Valid research in these areas will require marine reserves in which fishing effort and methods can be manipulated in collaborative studies involving fishers, researchers, and resource agencies.

Erstad, P. S, S. J. Jeffries, and D. J. Pierce. 1994 preliminary report for areas 7 and 7A Puget Sound fishery observer program: non-treaty sockeye gillnet fishery. WDFW. 1994.

Keywords: marine birds//salmon//harvest//harvesting impacts

Abstract: Study objective was to determine the nature and extent of marine mammal and marbled murrelet interaction with commercial salmon gill net fishing gear.

Evanson, Joseph R., and Joseph B. Buchanan. Winter Shorebird Abundance at Greater Puget Sound Estuaries: Recent Census Results and Identification of Potential Monitoring Sites. Puget Sound Research Proceedings; 1995 Jan 12-1995. Bellevue, WA. PSWQA. 1995.

Keywords: marine birds//Puget Sound

Abstract: This paper reports on a shorebird counts at 59 sites in the greater Puget Sound area, Hood Canal and the Strait of Juan de Fuca. Kilisut Harbor was the only site in eastern Jefferson County to have over 1,000 shorebirds. The high count at Kilisut was 1646 in 1992-93 counts and 796 in 1993-94. Sites with greater than 1,000 shorebirds are considered important for conservation and monitoring purposes. Sites with less than 5,000 shorebirds were found to support 27% of the winter population in both years of the study. Many disturbance factors threaten shorebirds and their winter environment. Most sites with over 1,000 birds occur in a cluster situated near major shipping channels, oil refineries and industrial centers. This makes such populations highly vulnerable to impacts of environmental pollution and habitat loss.

Everitt, R. D., C. H. Fiscus, and R. L. Delong. Northern Puget Sound Marine Mammals. Washington, D.C. DOC/EPA Interagency Energy/Environ. R&D Program. 1980. Doc. EPA-60099/78-80-139. U.S. EPA.

Keywords: marine mammals//Puget Sound//northwest straits//straits//seals

Abstract: Baseline study of marine mammals of northern Puget Sound and Strait of Juan de Fuca from November 1977 to September 1979. Emphasizing certain aspects of the biology of the harbor seal, which is the most abundant marine mammal in these waters. Additionally, abundance and distribution for 21 species of marine mammals is presented. Spring and summer months are the period when marine mammals in these waters may be most vulnerable to environmental perturbations. Study areas of importance in descending order are: eastern Strait of Juan de Fuca, San Juan Islands, eastern bays, tideflat areas, and western strait of Juan de Fuca. Of the 5 species of pinnipeds present, only the harbor seal occurs throughout the year in significant numbers. The largest numbers of animals hauled out during late summer-early fall

The Calif. and northern sea lion were both present seasonally. Less than 300 sea lions. 15 species of cetaceans included gray whale, minke whale, killer whale, harbor porpoise and Dall's porpoise. The river otter is common throughout the year in most parts of the study area.
Feist, Blake E. J. J. Anderson R. Miyamoto, University of Washington, Fisheries Research Institute, School of Fisheries. Potential impacts of pile driving on juvenile pink (Oncorhynchus gorbuscha) and chum (O. keta) salmon behavior and distribution. May 1992; FRI-UW-9603.

Keywords: pile driving/juvenile salmon/pink salmon/salmon behavior/salmon distribution/juvenile salmon impacts

Abstract: A pilot study assessed the potential effects of pile driving activities on the behavior and distribution of schools of juvenile pink and chum salmon. Sites studied included the Everett Homeport (near the mouth of the Snohomish River), Elliott Bay Marina (Seattle), and the Kingston and Bremerton Ferry Terminals. School size, frequency of occurrence, species distribution, and general fish behaviors were measured at the sites where pile driving and fish presence coincided. Individual fish were sub-sampled for total length, weight, and stomach contents. On sampling days, tidal stage, weather, salinity, and the underwater acoustic environment were also measured.

Pile driving did not occur at the Kingston site, and juvenile Pacific salmon were not present at the Bremerton site when pile driving was in progress. Therefore the data form these sites do not provide direct information on the impacts of pile driving on juvenile salmonids. Very few fish were observed at the Elliott Bay site, with or with out pile driving.

The majority of results regarding the impacts of pile driving on juvenile salmonids ecology are form the Everett Homeport site. The following encapsulates the results: 1) within the range of salmonid hearing, the sound field generated by pile driving activities had a radius of at least 600 m.; 2) pile driving operations apparently affected the distributions and general behavior of fish schools about the site; 3) nearly twice as many fish schools were found on the construction side of the site on non-pile driving days compared to driving days; 4) fish schools were typically in water <1.5 m, within 2m from shore, and they were surface oriented. Fish school distances form shore did not change significantly as a result of pile driving. Average total length of fish did not increase significantly over the study period, suggesting fish were either transient and/or not growing. Stomach content analysis indicated that most fish were feeding, and while salinity and tidal stage probably affected the vertical distribution of fish in the water column, it did not appear to alter fish behavior or distribution about the construction site as measured in this study.

Forney, K. A., J. Barlow, M. M. Muto, M. Lowry, J. Baker, G. Cameron, J. Mobley, C. Stinchcomb, and J. J. Carretta. U.S. Pacific Marine Mammal Stock Assessments: 2000. NOAA/NMFS. 2000. Draft.

Keywords: marine mammals//Puget Sound//northwest straits//straits

Abstract: Description of the stock's geographic range, a minimum population estimate, current population trends, current and maximum net productivity rates, optimum sustainable population levels and allowable removal levels, and estimates of annual human-caused mortality and serious injury through interactions with commercial fisheries and subsistence numbers. This information is used to evaluate the progress of each fishery towards achieving its goal of zero mortality and serious injury.

Fresh, K. L. B. Williams D. Penttila. Overwater Structures and Impacts on Eelgrass in Puget Sound, Washington. Puget Sound Research '95; 1995 12; Bellevue, WA. Olympia, WA.

Keywords: Puget Sound/overwater structures/habitat impacts/eelgrass/impact assessment

Abstract: STUDY OBJECTIVES: Impact Assessment. Determine if small single-family residence docks cause a decline in eelgrass densities under and adjacent to piers and assess if the use of gratings mitigate the impacts. METHODS: Empirical: eelgrass density was measured under and adjacent to a selection of seven "single- family" dock sites in Puget Sound from Roche Harbor to South Hood Canal. Baseline measurements and one year of post-project monitoring were also taken for five sites to assess effectiveness of mitigating impacts with grating. OBSERVED DENSITY DECLINES: Six out of the seven sites selected to measure declines without mitigating construction methods demonstrated measurable declines and/or absence of eelgrass growing under the docks. The one site that did not show measurable impact appeared to have a mitigating aspect to its structure as the dock moved up and down and side to side with tidal fluctuations. Four of the five structures evaluated for alternative mitigating construction methods demonstrated eelgrass densities decline when compared to undisturbed reference areas. At the fifth structure site, eelgrass density increased but increased substantially less than it increased in the reference area. COMMENTS: Preliminary results support the hypothesis that shading is the major cause of eelgrass density loss. This is demonstrated by significant reductions in density under docks and diminished reductions under docks with grating used to mitigate shading impacts. Structure length, height over the bottom, design, orientation, and local environmental conditions (i.e. current patterns) may also play a role in the nature and extent of impact.

Fresh, Kurt L. Distribution and abundance of fishes occurring in nearshore surface waters in northern Puget Sound. Seattle, WA: UW; 1979.

Keywords: nearshore//fish//Puget Sound//salmonids//salmon//rockfish// cod//lingcod//bottomfish

Abstract: Fishes occurring in the nearshore surface waters of northern Puget Sound, Washington were studied during 1974-1976 using a two-boat surface trawl (townet). Five sites, each representing a different habitat type were sampled in each of three geographic areas. Study objectives were to document the abundance, spatial and temporal distribution of fishes occurring in nearshore surface waters of northern Puget Sound. Nearshore surface waters were utilized as nursery and rearing areas by numerous fish species. While the townet was designed to sample larvae, larval fish were caught abundantly, primarily in spring. Mainly juvenile fish were found throughout the entire year in nearshore habitats. Few large fish were caught, perhaps because of avoidance. Of the 71 fish species captured, the 6 most abundant species comprised 98 percent of the total numerical catch. Twenty species were schooling whereas 51 were demersal; schooling species generally were more frequently occurring and more abundant than non-schooling species. Catches of most species were highly seasonal and indicated a lack of permanent resident species. Young-of-the-year Pacific herring were the dominant fish species occurring in nearshore surface waters. Herring catches were especially large at sites associated with protected eelgrass bays and in areas near known spawning grounds. Maximum catches of herring occurred during the spring and summer whereas minimum catches occurred in the fall and winter. Other abundant species included young-of-the-year Pacific sand lance, juvenile and adult threespine stickleback, larval to adult surf smelt, and larval to adult longfin smelt. While numerically not abundant, juvenile salmonids (mostly chinook salmon) occurred consistently in spring and summer primarily in the Cherry Point and Anacortes areas. The dominant nearshore pelagic species were present throughout the various nearshore habitats of northern Puget Sound with little evidence of distinct assemblages in different habitats. However, even though the dominant species exploit the entire nearshore spectrum of habitats, there were preferred habitats and areas.

Garrison, Kathryn J. and Bruce S. Miller. Review of the early life history of Puget Sound fishes. Seattle, WA: University of Washington, Fisheries Research Institute, School of Fisheries; 1982.

Keywords: juvenile fish/Puget Sound/life-history strategies

Abstract: This report reviews the early life history information of Puget sound fishes through 1981. Include distribution, reproductive timing and larval identification.

Gillespie, G. E. and Westrheim, S. J. Synthesis of information on marine fishes utilized as prey by marine and shoreline birds of the Queen Charlotte Islands. Vermeer, K. and Morgan, K. H. eds. The Ecology Status and conservation of Marine and Shoreline birds of the Queen Charlotte Islands. Ottawa, CA. Environment Canada. Can. Wildl. Serv. 1997. no. 93, pp. 36-55.

Keywords: seabirds//sea birds//birds//straits

Abstract: This synopsis lists the birds reported to prey on marine fishes off the Queen Charlotte Islands, British Columbia, and provides an abbreviated account of the prey with respect to their habitat, abundance, life history, commercial importance, and avian predators. In total, 50 avian predators were reported. All preyed on pelagic fishes; 14 preyed on demersal fishes; and 221 preyed on inshore fishes. Twelve species preyed upon all three groups. Seventy-eight different prey were reported -- 62 identified to species, six to genus, nine to family, and one to order. Pacific herring Clupea pallasi attracted the most avian predators (40 species), particularly during inshore spawning and early life history stages. In many cases, predation on inshore and demersal species was during their early life history stages, either as pelagic larvae or juveniles or as recently settled juveniles in shallow water.

Golding, Steven. Port Townsend Paper Corporation November/December 1993 Class II Inspection. Olympia, WA: WA Dept. of Ecology; 1994 Sep. Publication No. 94-147. (Water Body No. WA-17-0030).

Keywords: NPDES permits/polllutants/bioassays/outfall/water quality/sampling procedures

Abstract: A Class II Inspection was documented at the Port Townsend Paper Company pulp and paper mill just south of Port Townsend, Washington between November 15-17 in 1993. Related sediment sampling was conducted December 15. The combined process water and sanitary discharges met all NPDES permit requirements. The sanitary effluent was also well within all permit requirements. All VOA and BNA compounds found were within applicable EPA water quality criteria. No pesticide/PCD compounds were found in the influent or effluent. Five priority pollutant metals were detected in the effluent. Copper was found in an estimated concentration of over four times Ecology water quality criteria. The fathead minnow chronic test and bivalve larvae test demonstrated sensitivity to the pulp mill effluent. No VOA compounds were detected in the sediment samples. All BNA compounds and metals detected were below Ecology Marine Sediment Quality Standards. No toxicity was found in the Microtox test. Amphipod test results found one sample equal to 25 percent toxicity.

Goodwin, Lynn. Age, recruitment and growth of the geoduck clam in Puget Sound. WDFW. 1988. WDFW Prog. Report #215.

Keywords: shellfish//geoducks//Puget Sound

Abstract: This report describes the methods we used to collect geoducks, age the shells and estimate growth and recruitment rates. A discussion of the methods is discussed. Most shells used for age and growth determinations were collected from unharvested geoduck beds form 1979-1982. All samples discussed in this report were taken in water depths of between 10 and 20 meters. Many locations throughout Puget Sound were sampled. From 1970 to 1987 samples were taken to estimate recruitment in harvested and unharvested geoduck beds in small plots extensively disturbed by a venturi suction dredge.

Healy, M. C. Juvenile Pacific salmon in estuaries: the life support system. In: Kennedy V.S. (ed.). Estuarine Comparisons. New York. Academic Press. 1982.

Keywords: salmon//Puget Sound//estuaries//fish

Abstract: Three species of Pacific salmon (chum Oncorhynchus keta, chinook Oncorhynchus tshawytscha and coho Oncorhynchus kisutch ), spend significant time rearing in estuaries following their seaward migration. Chum are abundant in estuaries for two months in early spring, coho for two months in late spring, and chinook throughout the spring, summer, and autumn. The specific habitats occupied by each species vary with the size of the fish, the stage of the tide, and the time of year. Tidal creeks through marshes, the junction of major and minor distributaries in the intertidal zone and the delta front are favored habitats. The diet of juvenile salmon in estuaries reflects a mixture of preference and availability, and the availability of food varies significantly between years and between estuaries. Major prey tend to be highly concentrated in the boundary layer at the mudwater interface, and many are detritus feeders, indicating that the food web leading to juvenile salmon is detritus based. The value of an estuary as rearing habitat for juvenile salmon appears to be influenced by delta configuration and by the efficiency with which allochthonous organic carbon is trapped.

Henwood, Bill J. Barr and K. Morrison. A marine protected areas strategy for the Pacific Coast of Canada . Puget Sound Research '98. Seattle, WA. Olympia, WA. PSWQAT. 1998.

Keywords: MPA's//marine protected areas

Abstract: This paper describes the development of an integrated strategy for the establishment of a comprehensive MPA system along the Pacific Coast of Canada. Parks Canada, BC Parks, the Dept. of Fisheries and Oceans, the BC Land-Use Coordination Office, Environment Canada and BC Ministry of Agriculture, Fisheries and Food have collaboratively developed a draft proposal describing the following: a common vision and definition of MPA's; common goals and objectives for an MPA system; guiding principles for the establishment and management of MPA's; possible management regimes and designations of MPA's, and a proposed process for the identification, evaluation, establishment and management of MPA's. A series of stakeholder forums have been held in three coastal communities to discuss these proposals with a wide variety of stakeholders. Implementation of the strategy will be linked with coastal area management planning.

Hirschi, Ron. Critical Nearshore Habitats-Tala Point to Kala Point, Jefferson County. Jefferson County, WA. Jefferson County Planning Department and National Oceanic and Atmospheric Administration. 1999. Report to Jefferson County Planning Department.

Keywords: habitat//critical habitat//Jefferson County//Port Townsend//Tala Point// Kala Point//surf smelt//sand lance//fish//salmon//juvenile salmon//marsh//drift cell//shoreline/nearshore//Chimacum Creek//Port Ludlow//Port Ludlow Bay//eelgrass//intertidal//Ludlow Creek//spawning//juvenile fish//prey resources//Olele Point/bald eagles//Little Goose Creek//Oak Bay//shorelines//fish

Abstract: This report provides locations of critical habitats, including eelgrass beds, salt marshes, stream mouths, and documented spawning beds of sand lance, surf smelt, and herring. and documented salmonid use. Eelgrass beds were mapped with the aid of aerial photos, boat surveys, and beachwalks undertaken during this study. The purpose of the report is to further an understanding of the inter-related nature of these nearshore habitats and species, locational information is discussed in relation to several shoreline segments. Each segment corresponds to drift cells identified by geologist Johannessen.

Hixon. Mark. A. and B.N. Tissot. Fish Assemblages of Rocky Banks of the Pacific Northwest. U.S. Dept. of the Interior, Minerals Management Service, Pacific OCS Region. 1992. OCS Study MMS 92-0025. Final Report-Supplement.

Keywords: fish//rockfish

Abstract: This report characterizes the benthic habitats and fish assemblages at Stonewall Bank Oregon by describing associations of bottom types, visually dominant invertebrates, and demersal fishes. Rockfish densities were correlated to bottom type, stations, and general behavioral patterns. Fish abundance was also compared between day and night.

Hueckel, G. J., R. M. Buckley and B. L. Benson. Mitigating rocky habitat loss using artificial reefs. Bull. Mar. Sci. 44:913-922.

Keywords: rocky reef//mitigation//habitat//fish

Abstract: An artificial reef was constructed on a featureless sand bottom as mitigation for the man-caused loss of rocky-type subtidal habitat in Elliott Bay, Puget Sound, Washington from a shoreline development (fill) project. Using a list of indicator biota developed for this region, it was predicted the mitigation reef would develop a greater number of economically important fish species and greater diversities of sessile and epibenthic biota assemblages than the development site. The design of a 1:2 ratio of reef material: sand bottom accommodated the trophic level relationships normally occurring for fishes feeding from reef structures and surrounding natural habitats. The mitigation reef met the predicted development during the reef's first 8 months of submergence.

Hulsman, Steven G. and W. A. Palsson and G. J. Hueckel. An Annotated Bibliography of Puget Sound Nearshore Habitat and Marine Fish Life History Studies. Olympia, WA. Washington State Dept. of Fisheries. 1986. Technical Report 91.

]Keywords: marine biota/fish/nearshore habitat/marine life history strategies/recreational fishery/lingcod/herring/Strait of Georgia/pollution/sole rockfish/greenling/enhancement structures/Puget Sound/water quality/salmon/cod/impact assessments/surf smelt/invertebrates/fish ecology/shellfish

Abstract: An annotated bibliography of 188 references on Puget Sound nearshore habitat and marine life history studies.

Janzen, C. D. and L. B. Eisner. Marine Water Column Ambient Monitoring Program: Annual Report for Wateryear 1991, Final Report. Olympia, WA: Department of Ecology. 1993: 93-13.

Keywords: water quality//Puget Sound//Jefferson County//Port Townsend//habitat

Abstract: During Wateryear 1991 (October 1990 through September 1991), the Washington State Department of Ecology monitored water quality monthly at 28 stations in Puget Sound, four stations in Grays Harbor, and five stations in Willapa Bay. Of the 28 stations in Puget Sound, 23 sites showed dissolved oxygen concentrations below the water quality standards for marine waters one or more times, and 11 exceeded fecal coliform counts of 14 organisms/100 milliliters (mL) one or more times. Nutrient depletion was observed at 20 Puget Sound stations. Of the nine coastal stations, none violated dissolved oxygen standards, and four exceeded fecal coliform counts of 14 organisms/100 mL one or more times. Nutrient depletion was only observed at the Willapa Bay stations. Stations that did not experience nutrient depletion as defined by this report, were well mixed and lacked observable ongoing density stratification. At several Puget Sound stations, chlorophyll a concentrations were inversely proportional to nutrient concentrations, with maximum chlorophyll a concentrations and minimum nutrient concentrations observed simultaneously. Chlorophyll a concentrations were highest during the spring and summer months and lowest during late fall and winter months for Puget Sound stations. The coastal stations exhibited two chlorophyll a peaks, one during mid-summer and again in midfall. To assess the quality of the marine water column data, a detailed quality assurance assessment was conducted on the Wateryear 1991 (WY 1991) results. Ninety-four percent of the nitrite results were below detection limits. Discontinuing dissolved nitrite analysis until lower detection limits can be achieved was recommended. The quality assurance assessment also revealed that the fecal coliform bacteria results did not achieve precision objectives in either the field or laboratory replication. Procedures for future collection and analysis of fecal coliform bacteria should be amended to improve the quality of these data. In general, to improve temporal and spatial coverage for shorter term and episodic water quality events not caught by the monthly sampling component of the program, continued monitoring efforts should include a seasonal monitoring component. Sites showing signs of nutrient depletion and/or conditions that promote biological activity (stratification) should be priority candidates for seasonal monitoring.

Johannessen, Jim. Critical Shoreline Areas Relative to Critical Nearshore Habitats at Tala Point to Kala Point, Eastern Jefferson County, Washington. 1999. Jefferson County Planning Department and National Oceanic and Atmospheric Administration. Grant No. G9900057 NOAA/CZM/DOE.

Keywords: geology//drift cells//Tala Point//Kala Point//Olele Point//feeder bluffs//eastern Jefferson County//Jefferson County//Port Townsend

Abstract: This report was prepared to support a parallel effort of nearshore habitat mapping and characterization titled Critical Nearshore Habitats, Tala Point to Kala Point, Jefferson County, by Ron Hirschi (1999). Much of the field observations for the two studies were conducted simultaneously by boat or on foot. Similarly, the focus and conclusions of the two studies were reached cooperatively. Therefore, each report should be used in conjunction with the other, as the intent was for each of the two elements to augment each other and provide mapped features representing the conclusions of the multi-disciplinary effort.

Accompanying this report are three original USGS 71/2 minute quadrangles (Port Ludlow, Nordland, Port Townsend, South) that contain mapped critical shoreline areas discussed in the text. Portions of these three maps are reproduced within the report for convenience. Information on geology and coastal processes were compiled from existing published reports and maps as referenced, along with observations made while visiting the entire shore of the study area in the winter of 1998-99 and earlier. The study area for the project ran form Tala Point (east of Port Ludlow Bay) in the south end to Kala Point (in Port Townsend Bay) in the north.

Johnson, O. W., W. S. Grant, R. G. Kope, K. Neely, F. W. Waknitz, and R. S. Waples. Status Review of Chum Salmon from Washington, Oregon, and California. Northwest Fisheries Science Center, Seattle, WA: National Marine Fisheries Service. 1997. NOAA Technical Memorandum NMFS-NWFSC-32.

Keywords: salmon/estuaries//Puget Sound//nearshore habitat//life history strategies//prey resources//migration//Endangered Species Act/ESA/ESU//chum//summer chum//Washington//Oregon//California//fish

Abstract: This report reviews the ESA evaluation for chum salmon populations in the Pacific Northwest. It presents species and ESU definitions, listing petitions, and all aspects of chum biology. The biological description includes physical and biological features with life history and ecological information. It examines and presents in-depth descriptions of all life-history stages, regional distributions, hatchery production, practices, and influences, stock abundances, history, and trends.

Karp, W. A. Biology and management of Pacific cod (gadus macrocephalus) in Port Townsend, Washington. 1982. PhD. Dissertation.

Keywords: cod//Pacific cod//Port Townsend//Puget Sound//bottomfish// groundfish//fish//Jefferson County

Abstract: Pacific cod migrate into the waters of Port Townsend Bay during the winter. An intense commercial set net and trawl fishery is directed at these Pacific Cod spawning aggregations. Life history parameters estimated during this study were consistent with those expected from a fast growing, early-maturing stock close to the southern limit of its range. Growth analysis of length frequency data and tag returns provided length-at-age estimates of 27.0, 43.5, 55.5 and 64.2 cm at ages of 1,2,3, and 4 years. Population estimates indicated that there were about 14,000 fish in the bay when the fishery began. The population increased rapidly and reached a peak of more than 1100,000 fish within 10 days of the start of the fishery. Peak abundances were observed for approx. 1 week and then a gradual decline in the population size was observed. Seven weeks after the fishery began, population size was estimated to be 35,000 fish. Between 15-20 percent of the cod present in the bay on a given day emigrated or were caught during the subsequent 24 hours. Between 359,000 and 510,000 fish migrated into the bay during the season and 24 to 34 percent were harvested. The set net gar was more effective in harvesting larger fish, especially females.

Karp, William and B. S. Miller (University of Washington. College of Fisheries. Final Report to U.S. Navy). Pacific Cod (Gadus macrocephalus) studies in Port Townsend Bay, Washington. Seattle, WA. University of Washington, College of Fisheries. 1977 Aug; FRI-UW-7723. December 1976-August 1977.

Keywords: Port Townsend//Pacific cod//cod//fish//prey resources//substrate// Jefferson County

Abstract: Egg, larval, juvenile, and adult stages of the Pacific cod (Gadus macrocephalus) were sampled form the waters of Port Townsend Bay to provide information concerning the life history and fisheries biology of this species. Trawl sampling, carried out in January and February 1977, provided material for the determination of basic statistics, age structure, stomach contents, and fecundity. The trawl-caught fish were found to be fast growing, early maturing, and with short lifespans. Estimated fecundity at length was greater than published values for populations from more northern waters. Preferred food items were shrimp and small fish. Icthyoplankton sampling was carried out on seven occasions from February through June 1977. Gadoid (cod family) larvae were identified form many of the samples but poor documentation of the early life history of Pacific cod precluded positive identification of these gadoid larvae to species. It was suggested that gadoid larvae observed in late April were probably Pacific cod, based on spawning time and published rates of development. Attempts to rear Pacific cod eggs and larvae were not successful but the experiments did confirm reports that the eggs are demersal. Diving operations failed to encounter spawning adults or eggs. Eggs were not detected from a series of bottom grab samples. Juvenile Pacific cod were identified from trynet samples taken in northern Kilisut Harbor and along the northwest shore if Indian Island in mid-June 1977.

Kent, M. and R. Elston. Toxicopathic Liver Disease of Pen-Reared Salmon in Port Townsend Bay-1988 Studies. 1989. 89-148.

Keywords: fish//water quality//Port Townsend//Jefferson County//Puget Sound//salmon

Abstract: This report presents the results of an investigation in the occurrence of severe liver disease and 100% mortality observed in Sea Farm Washington's pen-reared Atlantic salmon in Port Townsend Bay in the summers of 1986 and 1987. A long-term bioassay of Atlantic salmon using mill effluence indicated that the pulp mill was not the likely source of the presumed toxicant. The disease has also occurred at several net-pen sites in BC but does not appear to be associated with chemical contamination. It was suggested that the disease could be caused by a natural toxin, possibly an algal toxin, this hypothesis requires further testing. Chemical analysis of affected liver and muscle tissues, sediments, effluents, and the water column in separate but coordinated studies did not identify toxicants of likely significance. Such liver disease in at least three salmonid species at several sites in the Pacific Northwest identify the conditions as a significant limiting factor to successful net-pen culture in particular Pacific Northwest locations. Coho net-pen operations in Port Townsend Bay did not appear to be affected, neither were non-salmonid fishes such as surfperch and English sole. Small chinook were also found to be affected.

Kyte, M. A. (Ardea Enterprises). The Nongame Marine Invertebrates of Washington: An Inventory of Species and Sources of Loss with a Status Evaluation and Management and Conservation Guidelines. Snohomish, WA. 1989.

Keywords: invertebrates//nongame//invertebrates//worms//anemones//leeches//
chitons//snails//oysters//octopus//nudibranchs//clams//mussels//bivalves// invertebrate management//species status//shellfish

Abstract: This report presents an examination of nongame marine invertebrates (NGMI) situation for effective conservation and management. This report overviews NGMI in Washington waters, sources of losses, species status, and conservation guidance. Although the quality of Puget Sound may be improving through agency efforts and a concerned public, individual invertebrate species and communities are disappearing or are threatened over large part so their ranges. Direct sources of loss include: collecting for teaching by schools, collecting for schools by commercial supply companies, collection for research or bioassays by scientists, collecting for public aquarium, harvesting for subsistence by citizens, collecting for bait to catch other species and collecting for souvenirs. Indirect sources of loss include: derelict commercial fishing gear, especially gill and seine nets, sport and commercial harvesting, water and sediment quality pollution, commercial developments with activities such as dredging, pile driving and log rafting, walking and vehicle driving in the intertidal.

Lash, Jennifer and M. Solin. In: (eds) P.G. Wells and P.J. Ricketts The role of No-Take Marine Protected Areas in Facilitating Coastal Zone Management in British Columbia. Canada Coastal Zone '94 Cooperation in the Coastal Zone: Conference Proceedings. Sept. 20-23. Halifax, NS

Keywords: Marine protected areas

Abstract: Canada does not have a national policy for the management of the coastal environment. Attempts to create and implement a policy have been futile due to the lack of public pressure and political will. Increasing public interest and concern in the marine environment can help motivate the political will. Public requests for increased marine protection has been successful in various states in the US and has become an effective tool in BC. The establishment of Whtyecliff Park in West Vancouver as a No-Take marine protected area was the direct result of a community initiative combined with academic and legal advisers. The establishment of no-take MPA's play a crucial role in developing a coastal management policy. Establishing a network of public initiatives will increase public awareness of the ocean as well as motivate the government to take action towards creating a national Coastal Zone Management Policy.

Laufle, J. C. Biological development and materials comparison on a Puget Sound artificial reef. 1982. Wash. Dep. Fish. Tech. Rep. 72.

Keywords: fish//reefs//artifical reef//rockfish//bottomfish//groundfish//Puget Sound

Abstract: Using SCUBA techniques, artificial reef colonization by algae, invertebrates, and fishes is documented. Habitat comparisons are made between different reef types. Diel and seasonal abundances are discussed. Lingcod nesting was observed. The topic of deployment and management of artificial reefs is discussed.

Lemberg, Norm A., M. F. O'Toole, D. E. Penttila, and K. C. Stick. 1996 Forage Fish Stock Status Report. Olympia, WA. WDFW. 1997.

Keywords: fish//puget sound

Abstract: The objective of this report is to provide an evaluation of current marine forage fish stock status in Washington. The significance of forage fish in the diet of many important marine fish is discussed. This report provides Puget Sound stock status profiles, stock status summaries for 1994 and 1996, a cumulative herring spawner biomass graph for 1977-96, annual natural mortality, and herring fisheries landing information followed by a synopsis for coastal herring.

Lemberg, Norm A. S. F. Burton and W. Palsson. Hydroacoustic results for Puget Sound herring, whiting, and Pacific cod surveys, 1986-1987. Olympia, WA: State of Washington, Dept. of Fisheries; 1988.

Keywords: fish//Puget Sound//herring//whiting//cod//bottomfish//groundfish

Abstract: Reports assessments in South Puget Sound, Northern Hood Canal, Strait of Georgia and Port Susan Northern Hood Canal is area between Hood Head and Port Gamble. Area covered was not as far north as Port Townsend.

Llanso, R. J., S. Aasen, and K. Welch. Marine Sediment Monitoring Program 1. Chemistry and Toxicity Testing 1989-1995. Olympia, WA. 1998 Aug. Publication No. 98-323. Entire Puget Sound, West to Port Angeles and North to Canadian US border. Includes Strait of Juan De Fuca Haro Straits, Strait of Georgia, Admiralty Inlet, Port Townsend Bay, Discovery Bay, and Dungeness subestuary.

Keywords: sediments//Puget Sound//invertebrates//Jefferson County//Hood Canal// lead/zinc/PCBs/DDT/Puget Sound/cadmium/chromium/copper/silver/mercury/arsenic/

Abstract: Reports results from baseline sediment monitoring of conditions and trends throughout Puget Sound for the period 1989-1995. Data was collected annually at eighty-six stations throughout Puget Sound, Hood Canal, Strait of Georgia, and Strait of Juan de Fuca. Stations included Port Townsend Bay, southwest shore of Indian Island, and Discovery Bay. Target chemicals included antimony, arsenic, cadmuim, lead, selenium, silver, thallium beryllium, chromium, copper, nickel, zinc, mercury, aluminum, barium, calcium, cobalt, iron, magnesium, manganese, potassium, sodium, and vanadium. These include aromatic and chlorinated aromatic compounds, ketons, ethers, esters and carbon disqulfide and semivolatile organics, phenols chlorinated and nitro-substituted phenols, resin acids and low molecular weight polycyclic and chlorinated and aromatic hydrocarbons were amongst the contaminants identified and measured. Port Townsend was listed as one of ten stations having contaminated concentrations above state standards in any one year, which in the case of Port Townsend was 1989 only. Port Townsend also showed the presence of arsenic and nickel. Nickel was present in all years except 1995. Discovery Bay showed arsenic in 1994 only. These are the levels at which adverse biological effects are expected to occur. This was due to a high concentration of the resin bis(2-ethylhexyl)phthalate and dehydroabietic acid.

Llanso, R. J., S. Aasen, and K. Welch. Marine Sediment Monitoring Program II. Distribution and Structure of Benthic Communities in Puget Sound 1989-1993. Olympia, WA: Washington Department of Ecology. 1998 Entire Puget Sound, Strait of Juan de Fuca west to Port Angles, Georgia Strait north to U.S./Canadian border, and Georgia Strait

Keywords: sediments//Puget Sound//invertebrates//Jefferson County//Hood Canal//benthos

Abstract: Reports baseline data on contaminated and uncontaminated stations and evaluates condition of benthic macro-invertebrates in relation to toxic chemicals in sediments throughout Puget Sound, Hood Canal, and the Straits of Georgia and Juan de Fuca between 1989-1993. Stations included Port Townsend Bay, southwest shore of Indian Island, and Discovery Bay. Multivariate analysis techniques shoed that infaunal assemblages in Puget sound are primarily related to sediment composition and water depth, and secondarily to geographical location. This study represents the first system-wide effort to characterize benthic assemblages in the Puget Sound region.

Long, E., J. Hameedi, A. Robertson, M. Dutch, S. Aasen, C. Ricci, and K. Welch. Sediment Quality in Puget Sound: Year 1, Northern Puget Sound. Olympia, WA. Department of Ecology. 1999.

Keywords: sediment quality//Puget Sound//contaminants//sediments

Abstract: As a component of a three-year cooperative effort of the Washington State Department of Ecology and the National Oceanic and Atmospheric Administration, sediments from 100 locations in northern Puget Sound were tested to determine their relative quality. The purpose of this survey was to determine the quality of sediments in terms of the severity, spatial patterns, and spatial extent of chemical contamination, toxicity, and alterations to benthic infauna. The survey area encompassed the region from Port Gardner Bay north to the US/Canada border, excluding the San Juan Islands. Surficial sediments were tested and analyzed from each of the 100 locations. Data from the chemical analyses indicated that toxicologically significant contamination was restricted in scope to a relatively small portion of the region. The spatial extent of relatively severe contamination varied considerably among chemicals. However, less than 2% of the area was considered "contaminated" for most substances. Sediments from several sampling locations within Everett Harbor often had the highest chemical concentrations. In addition, samples from some stations in Bellingham Bay and other locations scattered throughout the study area had elevated concentrations of some substances. Data from four kinds of toxicity tests indicated a similar pattern: the degree of toxicity was highest in samples from Everett Harbor followed by those from other locations scattered within the survey region. The spatial extent of significant toxicity ranged from 0% to 5% among the toxicity tests. Wide ranges in several numerical indices of benthic infaunal structure indicated good correspondence with tests of toxicity and the concentrations of numerous chemical substances. That is, there was evidence of altered benthic populations in some areas nearest urban centers. Chemical contamination and toxicity of sediments were less severe in northern Puget Sound than in many other estuarine areas studied in the U.S. by NOAA. Results from similar analyses of samples from the central Puget Sound (sampled in 1998) and southern Puget Sound (sampled in 1999) will be compiled with the data from northern Puget Sound, to provide a broad-scale evaluation and quantification of the spatial scales and patterns in sediment quality throughout the entire region.

SUBJECT WATERBODIES: Strait Of Georgia, Drayton Harbor, Bellingham Bay, Padilla Bay, Fidalgo Bay, Guemes Channel, Saratoga Passage, Penn Cove, Steamboat Slough, Port Gardner, Inner Everett Harbor, Ebey Slough, Skagit Bay, Similk Bay, Port Susan, Possession Sound, Strait Of Georgia, Drayton Harbor, Bellingham Bay, Padilla Bay, Fidalgo Bay, Guemes Channel, Saratoga Passage, Penn Cove, Steamboat Slough, Port Gardner, Inner Everett Harbor, Ebey Slough, Skagit Bay, Similk Bay, Port Susan, Possession Sound

Long, Edward R. A Synthesis of Biological Data from the Strait of Juan De Fuca and Northern Puget Sound. Seattle, WA.NOAA-Office of Marine Pollution Assessment.1983 Feb.D6-E693-EN and EHE625-A.

Keywords: biota//Strait of Juan De Fuca//Puget Sound/food web//migration//reproduction//natural stresses//habitats//communities//trophic interactions//species richness//fish//invertebrates//shellfish

Abstract: Summarizes the biological data collected during a five-year research project including information on marine fishes, food webs, migration, reproductive processes, natural stresses, major habitat types and their associated biological communities, trophic interactions, organism densities, biomass and species richness.

Lubchenko, S., Palumbi, and S. Gaines. Developing a Theory of Marine Reserves. NCEAS Project accessed at ttp://www.nceas.ucsb.edu/fmt/doc?https://www2.nceas.ucsb.edu/admin/db/web.plist
Keywords: MPA//marine protected area

Abstract: This is a multidisciplinary working group organized through NCE