Acknowledgments

The author would like to extend special thanks to the resource managers and marine resource committee members who helped make this report possible with their contributions of time, information, and comments, In particular, I thank the following persons for their special contributions and effort.

Joe Breskin - EnviroSearch

Judy D'Amore - Port Townsend Marine Science Center, Jefferson County MRC

Tim Determan - Washington State Department of Health

Larry Lawson - Jefferson County MRC

Mary Mahaffy - U.S. Fish and Wildlife Service

Lauren Mark - University of Washington, Wetland Ecosystem Team

Michelle McConnell - MRC Early Action Project Manager

Tom Mumford - Washington State Department of Natural Resources

Anne Murphy - Jefferson County MRC, Port Townsend Marine Science Center

Michael Murray - Channel Islands National Marine Sanctuary

Linda Newberry - Jamestown S'Klallam Tribe and Jefferson County MRC

Jan Newton - Washington State Department of Ecology

Jim Norris - Marine Resources inc.

David Nysewander - Washington Department of Fish and Wildlife

Andy Palmer - Jefferson County MRC

Wayne Palsson - Washington State Department of Fish and Wildlife

Dan Penttila- Washington State Department of Fish and Wildlife

Kevin Ryan - US Fish and Wildlife Service, Protection Island National Wildife Refuge

Anne Shaffer - Washington Department of Fish and Wildlife

Deborah Siefert - Jefferson County MRC and NOAA

Charles Simenstad - University of Washington, School of Aquatic and Fishery Sciences
 

Table of Contents

1. BACKGROUND AND PURPOSE.......................................................................5

Introduction and Methods.............................................................................5

2. OCEANOGRAPHY, WATER, AND SEDIMENT QUALITY.................................7

Characterization of the Resource.................................................................7

INTRODUCTION

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.

There is ample evidence that the Northwest Straits marine ecosystem and some if its marine resources are in serious decline with problems crossing geographical and jurisdictional boundaries. Bottom fish, forage fish, salmon, sea birds, invertebrates and some populations of marine mammals have declined precipitously since 1980. This depletion of marine resources has hurt economics and communities around the Northwest Straits. Existing management strategies, while sufficient in terms of legal authority, have failed to achieve the coordination and focus necessary to change these trends (British Columbia/Washington Environmental Coop. Council 1994; Wilson et al. 1994; Strickland et al. 2000).

This report summarizes the results of the Jefferson County Marine Resources Committee literature review and data search as to the status of marine resources in Jefferson County. Marine resources are separated into six categories: 1) oceanography, water and sediment quality; 2) nearshore habitats; 3) fish; 4) invertebrates; 5) birds, and 6) marine mammals.

METHODS

This literature review and data search was compiled using a preliminary list of information topics and sources following a review of the Northwest Straits Overview prepared by Washington Sea Grant for the Northwest Straits Commission and the Status of Marine Protected Areas in Puget Sound, Volumes 1 and 2, by Michael Murray (1998). Information was then collected from a review of the following databases for literature and data specific to the boundaries of the Jefferson County Marine Resources Committee. These include but are not limited to the following sources.

• NOAA Protected Resources Publications,
• Puget Sound/Georgia Basin Transboundary Bibliography,
• A collection of local and regional marine protected bibliographies,
• Washington State Department of Ecology water and sediment quality bibliographies, database, and monitoring results reports,
• NOAA Seattle Regional Library,
• NMFS status reviews,
• Washington Sea Grant Publications,
• Washington Department of Fish and Wildlife forage fish and groundfish fact sheets and related reports,
• Aquatic Sciences and Fisheries Abstracts (ASFA),
• UW Fisheries Research Institute Reports,
• National Technical Information Service (NTIS), and
• University of Washington Library databases.

2. OCEANOGRAPHY, WATER, AND SEDIMENT QUALITY

CHARACTERIZATION OF THE RESOURCE

Basin

The Jefferson County MRC boundaries include those marine waters defined as the Northwest Straits pursuant to the Murray-Metcalf Initiative. The boundaries of the Jefferson County area of the Northwest Straits include Olele Point at the south end in Hood Canal, San Juan County at the northernmost boundary; Island County at the eastern boundary, and Clallam County at the western boundary.

Figure 1. Northwest Straits Region (Source: People for Puget Sound)

Circulation

Circulation in the region consists of lower-salinity, warmer water from rivers flowing seaward at the surface with higher-salinity and colder water originating from the Pacific Ocean flowing landward along the bottom. The combined forces of lunar influence, climatic conditions and bathymetry determine the extent to which these layers are mixed. During neap tides, when the moon is in the first and last quarters and the tidal range is least, seawater intrusions and the influx of saltier water to lower Puget Sound is largest. During periods of spring tides, new and full moon, seawater intrusions into lower Puget Sound are less due to the increased mixing of freshwater with saltwater during high amplitude tides. Temperature, salinity and density differences between freshwater runoff and nutrient upwellings from ocean waters determine the extent of mixing which is influenced strongly by the surface force of wind (Cannon 1999). These forces combine to make the Strait of Juan de Fuca a well-mixed and wind-dominated system. Strong winds, deep waters, ocean intrusions, and currents coupled with riverine inputs result in the straits being well mixed, cold, and nutrient rich waters year-round. The presence of a shallow sill at the entrance to Admiralty Inlet, the narrow opening of the inlet, and the large volume of water passing through the inlet, magnifies the extent of this mixing. Strickland (1983) describes the sill at Admiralty Inlet as obstructing the continuous inflow of deep water thereby producing one of the dominant areas of mixing in the entire Puget Sound. It disrupts the inflow of seawater from the straits and diverts surface outflow back into the sound. For example, water entering the sound at a given river mouth might receive an infusion of ocean water at Admiralty Inlet. It may then be diverted back through the cold, dark depths of the main Puget Sound basin to the Narrows and spurt to the surface at that location. This could be repeated several times before the river outflow finally exits seaward. This strong mixing component produces well-mixed waters in Port Townsend Bay with higher dissolved oxygen levels than those smaller inlets and bays that do not receive the mixing forces of Admiralty Inlet (Strickland 1983).

In contrast to the mixing dynamics of Admiralty Inlet, water entering Discovery Bay is persistently stratified with colder, saltier, and denser water near the bottom and lower salinity and warmer waters at the surface. The combined effect of bathymetry, low wind-mixing, and low current exchange produces the seasonally stratified and poor flushing characteristics of Discovery Bay. This weak mixing and flushing produces conditions of low nutrient levels near the surface and low oxygen levels near the bottom (Newton 1998, Strickland 1983).

WATER QUALITY

Monitoring

The Washington State Department of Ecology (DOE) monitors marine water quality for depth, temperature, salinity, density, pH, fecal coliform, dissolved oxygen, light transmission, chlorophyll, phaeopigments, nitrites and nitrates, ammonium, orthophosphate, and fecal coliform bacteria at three stations in the Jefferson County portion of the Northwest Straits. One site is located just north of the entrance of Admiralty Inlet, one site is located in Port Townsend Bay and a third site is located just off of Mill Point in Discovery Bay. Both the Port Townsend Bay site and the Admiralty Inlet site are core sites monitored once per month every year. There are sixteen to nineteen such core monitoring stations in Puget Sound and six to thirteen rotational stations. Rotational stations are monitored on a prioritized basis based upon: suspected problems and insufficient data; lack of data in the presence of environmental and land-use features indicating potential problems; and by specific requests to aid environmental data or update outdated data. Discovery Bay is one of these rotating monitoring sites. It was monitored in 1997 and is now monitored in 2000 due to low dissolved oxygen findings in late summer and early fall of 1997. The sites at Admiralty Inlet and Discovery Bay are classified as seasonally stratified while the stratification of the site in Port Townsend Bay is classified as weak. A Jefferson County study reported that Snow Creek accounts for 99% of the suspended sediments entering Discovery Bay with most loading observed to during large storm events (Parametrix 2000). The Washington State Health Department (DOH) also monitors marine water quality in the sampling of shellfish in shellfish growing areas.

The Washington State Department of Health (DOH) and the Jefferson County Conservation District (JCCD) also monitor water quality in a number of streams draining into Hood Canal, Port Townsend and Discovery Bays. Those results have been consolidated into a technical assessment report (Parametrix 2000).

Joint Effort to Monitor the Strait (JEMS) - The Joint Effort to Monitor the Strait (JEMS) is a new DOE monitoring program consisting of a ship transect south of Cattle Point, across the strait towards Protection Island with samples taken at three stations. These stations will help monitor conditions in the strait relative to conditions in Puget Sound and other embayments such as Discovery Bay. The results are expected to reflect conditions in the nearby strait that correspond to conditions in adjoining waters (Newton 2000).

Results of Monitoring

Dissolved Oxygen - The condition of low dissolved oxygen (DO) also known as hypoxia is that level that is deleterious to many organisms. This is typically 0.5-3.0 mg/l or between 0.2-2.0 mg/l. However, as given the evidence that the behavior or fish, larvae and other organisms can be negatively affected by concentrations as low as 4-4.5mg/l, the level of 5 mg/l is considered the upper limit for biological stress due to low DO (Newton et al 1998). In 1997, Discovery Bay was one of five Puget Sound sites falling below 3 mg/l. As a consequence of this low DO, the bay is presently being monitored again for the year 2000. It is monitored using a seaplane and landing at Mill Point. The bay's stratification and high productivity level are likely major factors producing these low DO levels. Newton (1998) reports that the existence of any human impact on this DO level is unknown but that the persistence of this low DO should be regarded with caution.

July through September 1997 indicated low DO levels (less than 5 mg/l) at both Admiralty Inlet and Port Townsend Bay stations. However, these levels are typical for the Admiralty stations due to the influence of naturally low-oxygen ocean upwellings flowing eastward through the straits. It is a natural condition for deep oceanic water to measure low in DO due to isolation from the surface interface with oxygen and the consumption of oxygen in plant and animal respiration processes (Newton et al. 1998). Both of the Admiralty stations are located in deep water from 80-100 meters. The station inside Admiralty Inlet shows low DO much less frequently than the station outside. This is likely due to the mixing and aeration of water masses as water flows past the sill. See Appendix A Figure 1 for a map of dissolved oxygen results at Puget Sound monitoring stations.

Nutrients - Dissolved inorganic nutrients, forms of nitrogen and phosphorus (i.e. ammonium NH₄, nitrate NO_3, nitrite NO₂ and orthophosphate OPO₄^3-) are important to marine ecosystems for plant growth and the first trophic level of the marine environment. High Nitrite-N concentrations are eutrophication indicators. Dissolved inorganic nitrogen is considered the limiting nutrient in marine systems. Monitoring the levels of nitrogen, which reflect phytoplankton growth patterns, provides a baseline profile against which to compare changes over time and predict possible influences responsible for changed readings. Neither of the sites at Admiralty Inlet nor Discovery Bay sites indicated a limitation of nitrogen.

Ammonium-N concentrations are reflective of anthropogenic inputs. Stations with high ammonium-N concentrations could reflect sewage input. In 1997, the Admiralty Inlet sites did not reflect high ammonium-N. However, the Discovery Bay site did reflect high ammonium-N concentrations. The cause for this is still unknown. See appendix A Figure 2 for a map of ammonium-N findings.

Fecal Coliform Bacteria - Although not necessarily harmful in and of themselves, the presence of fecal coliform bacteria is an indicator of the potential presence of pathogenic bacteria or viruses that may also be present in a marine environment receiving inputs of the fecal coliform bacteria. As a crude estimate, measurements of 14 organisms/100 ml is interpreted to be an indicator of contamination concern and 50 organisms/100ml is in indication of potentially serious contamination (Newton et al. 1998). All of the Jefferson County sites reflected less than 14 organisms/100mL in1997 samples. See Appendix A Figure 3 for a map of fecal coliform findings.

The Washington State Department of Health participates in the Puget Sound Ambient Monitoring Program (PSAMP) efforts through the monitoring of marine water quality in selected shellfish growing areas. These include 21 stations in Discovery Bay, six stations in Port Townsend Bay, and 20 stations in Kilisut Harbor. See Appendix A Figure 4 for identification of commercial shellfish classifications in eastern Jefferson County. Also see discussions of shellfish status on pages 37-38 of this report (DOH 2000).

Eutrophication - A condition of eutrophication from increased nutrient supply to nutrient-limited stratified waters can result in large algal blooms and a subsequent low DO level in bottom waters. Continuous or intermittent hypoxic events can cause shifts in species composition with fish moving out of a low DO area or being more susceptible to disease (Smith et al. 1992).

The presence of stratification, low DO, and high nutrient levels are indicators of eutrophication status and eutrophication susceptibility. Discovery Bay is one of five Puget Sound stations showing hypoxia due to stratification, low DO and high ammonium concentrations (Newton et al. 1998). The stations on either side of Admiralty Inlet showed no susceptibility.

SEDIMENT QUALITY

Monitoring

Over the period of the last century, Puget Sound has been a major repository of municipal and industrial wastes, combined sewer overflows, storm drains, dumping operations, and chemical spills combined with urban and agricultural runoff. Such discharge and runoff sources have been found to carry heavy metals, polynuclear aromatic hydropcarbons (PAHs) and chlorinated hydrocarbons.

The Marine Sediment Monitoring Program (MSMP), implemented in 1989, measures sediment contaminants, evaluates biological conditions, and assesses the potential for sediment toxicity. By combining the analysis of benthic community structure with laboratory toxicity bioassays, the biological significance of actual and potential contaminant levels can be assessed. For example, studies of benthic communities in contaminated areas such as Everett Harbor have reported lower total abundances of individual species, lower species richness of pollution intolerant species, and higher incidence of pollution-tolerant species than outer harbor uncontaminated control stations (Long, et al.1999). Chemical compounds and metals identified in these studies include lead, zinc, silver, copper, mercury, cadmium, chromium, arsenic, polycyclic armoatic hydrocarbons (LPAH) polychlorinated biphenyls (PCBs), beta coprostanol, beta sitosterol, arsenic, copper, mercury, lead, zinc, anthracene, flouranthese, phenanthrene, pyrene, and DDT (Llanso et al. 1998).

Stations positioned pursuant to the Puget Sound Estuary Program (PSEP) recommended protocols thatare deliberately located away from major sources of pollution and in shallow areas at depths of 20 meters or less. This allows the characterization of background conditions and the highest total abundance of benthic organisms (MMC, 1988). There are a total of 76 monitoring stations in the combined northern and southern Puget Sound monitoring program. This includes the San Juan Islands, the eastern Strait of Juan de Fuca to Port Angeles, and north to the Canadian border. These include 34 core stations sampled annually and 42 rotating stations sampled on a three-year schedule. Four monitoring stations are within the Jefferson County Northwest Straits boundaries. These include Discovery Bay near Contractor's Point, Port Townsend Bay between Glen Cove and Whalan Point, and Oak Bay on the southern end of Indian Island. The station in Port Townsend Bay is a core station and the stations at Indian island and Discovery Bay are rotational.

Monitoring Results

Sediments were characterized by grain size, sulfide presence, and percentage of organic carbon content. Sediment oxygen depletion rates reflect the nature of chemical transformations and nutrient cycling occurring in particular sediments. Sediment organic carbon content reflects the ability of sediments to retain chemicals. The higher the percentage of organic carbon, the higher the capacity becomes to retain chemicals (Mitsch and Gosselink 1993). When water fills soil pore spaces, the rate at which oxygen diffuses through sediments is drastically reduced. The ability of soils or sediments to transfer oxygen is called the redox potential. This potential is reflected in the color of the soils with brown having a greater oxygen transfer potential and black having the lowest oxygen transfer potential. At the MSMP stations, Redox Potential Discontinuity (RPD) was estimated through measurements of the top brown layers of sediment ranging from less than 0.5 cm to greater than 2 cm. The thinner the brown layers of sediment the lower the RPD. The larger the brown layers, the larger the RPD. The Discovery Bay samples were composed of sand with a high redox potential of 3 on a scale from 1 to 4. The Port Townsend Bay site was composed of mud with a redox potential varying with the year from 3 to 4. The Oak Bay site, composed of mud, had a RPD of 2. None of these Jefferson County sites had detectable hydrogen sulfide. High concentrations of organic carbon were not found at any of these sites. See Appendix A Figure 5 and 6 for maps of DOE marine sediment monitoring stations and study areas. Data from these stations will be summarized annually and analyzed every five years to determine changes in sediment chemistry, toxicity, and community structure.

Contaminant Compounds - The Port Townsend Bay station was one of ten stations in the entire study area identified as contaminated by having contaminant concentrations above determined biologic thresholds indicating the potential for adverse biological effects for any one year (Llanso et al. 1998). This was due to high concentrations of the phthalate ester compound, bis(2-ethylhexyl)phthalate, and dehydroabietic acid. The highest concentration by far of the phthalate ester to occur in the entire study area occurred in Port Townsend Bay in 1989. The Port Townsend site showed concentrations of arsenics in 1990 and 1994. The Discovery Bay site showed arsenic only in 1994. The Oak Bay site showed the presence of beryllium and nickel in 1995. The Discovery Bay and Oak Bay sites were not included in these 18 sites. In summary, the range of contaminant concentrations at current monitoring stations was concluded to be low. The MSMP is designed for monitoring of ambient conditions and changes over time. It is not designed to evaluate areas of highest contaminant concentration and should not be used to identify "hot spots".

Biologic Contamination Assessment - The Apparent Effects Threshold (AET) values were assigned to stations using the survival of the amphipods (rhepoxynius abronis) in tested sediments. Only sediments from Port Townsend and Port Susan were found to exhibit mortality above 24.5% in more than one year (the anomalous data of 1990 was excluded). Amphipod results are compounded by the fact that amphipod survivability is determined by percent silt and clay as well as the presence of contaminants (Llanso 1998). In consideration of this sediment type effect, only Port Susan and Dyes inlet amphipod mortality appeared to be related to contamination at the Puget Sound monitoring stations. Appendix A Figure 7 maps DOE Marine Sediment Monitoring sites exhibiting contamination with potential biological effects. Only stations with five or more compounds are shown. Port Townsend is one of the contaminated stations

Industrial Contamination - The Port Townsend Paper Corporation November/December 1993 Class II Inspection Report described discharges as lying well within all permit requirements. No pesticides or PCB compounds were found in the influent, effluent or outfall adjacent sediments. Five priority pollutant metals were detected in the effluent. Copper was found in an estimated concentration of over four times the DOE acute marine water criteria. Although Daphnia magna and rainbow trout survival tests revealed no acute toxicity in effluent, fathead minnow showed reduced growth and survival and bivalvle larvae showed significant mortality and considerable abnormality. Such toxicity impacts to bivalve larvae are typically seen in pulp mill effluents. No toxicity was found by the Microtox test on sediment samples. However, the amphipod test showed significant toxicity near the outfall. As toxicity did not exceed 25%, the sediments were not designated as having an adverse effect. Significant toxicity in amphipod tests are typical of sediments near pulp mill outfalls. Recommendations from the study included: verification and assessment of copper in effluent and condition of receiving waters; insurance of maintenance protocol through record review of wastewater and sewage treatment plant, and a reduction in chlorine residual in the sewage treatment plant effluent to a concentration less than or equal to 1.0 mg/l if adequate disinfection could still be attained.

The 1998 DOE Washington State Dioxin Source Assessment Report defined dioxin sources as facilities engaged in incineration or wood-treating with pentachlorophenol, municipal and medical waste incinerators, municipal wastewater treatment, bleached pulp processes, cement kilns, use of hog-fuel boilers, and activated carbon regeneration. Municipal wastewater treatment plants can pass on dioxins in discharge from sources discharged to the plant. The report reviews the structure of such chemicals and the process of dioxin incorporation into the human and animal food web. Port Townsend Paper Corp. is listed as a potential source due to its operation as a hog-fuel burning facility. This potential as a dioxin source is somewhat magnified due to the implication of burning salt laden hog fuel derived from logs rafted on salt-water (Luthe and Prahacs 1993). EPA (1994) ranks wood waste boilers as the fifth largest dioxin producers among source categories. However, in Washington State it is likely that this category is more important due to: 1) timber-related industries representing a much larger portion of Washington commerce compared to other regions nationally; 2) the increased potential to use salt-laden hog fuel in Washington due to the practice of rafting logs on salt-water; 3) the prevalence of burning of other fuels in wood waste boilers including sludges from mill wastewater treatment plants; 4) chipped tires and used oil, and 5) the notion that EPA's national assessment based on the capacity of air emissions may underestimate the importance of this source due to the highest loads actually being associated with fly ash (Yake et al. 1998).

DATA GAPS and RESEARCH NEEDS

Water Quality

Long term monitoring in conjunction with the JEMS program monitoring in the straits is required to compare long-term trends in the straits to Admiralty Inlet, Port Townsend Bay and particularly Discovery Bay to further identify underlying factors in observed monitoring samples (Newton 2000).

The Port Townsend Marine Science Center (PTMSC 2000), with the participation of Port Townend High School District's eighth grade class, has been monitoring water quality, temperature, salinity, and dissolved oxygen concentrations at four sites in the Port Towsend Bay area for the last five years. These sites are Indian Point, Admiralty Inlet, South PT Bay, and Kilisut Harbor. PTMSC has also collected fecal coliform counts for Pt. Hudson and the Port of Port Townsend Boat Haven over the past five years. The results obtained from the water quality site at Admiralty Inlet and Kilisut Harbor are generally consistent with DOE monitoring results at Admiralty Inlet indicating that Port Townsend Bay meets Washington State marine water quality standards for temperature and DO with the exception of natural occurrences of low DO due to deep water oceanic upwellings at Admiralty Inlet and low DO and high temperatures occasionally at the Kilisut Harbor site due to sun energy transmission into shallow waters and little mixing due to limited circulation in the embayment. Such conditions can naturally produce warmer temperatures with warmer temperatures resulting in lower DO levels.

However, low DO and high temperatures at the Indian Point monitoring site between the ferry terminal and the Port of Port Townsend Boat Haven likely reflect anthropogenic impacts warranting further monitoring. The high fecal coliform counts measured at Pt. Hudson Marina and the Port of Port Townsend Boat Haven also indicate anthropogenic influence and provide further reason for continued contamination monitoring to track health risks associated with high bacterial counts Norris (1997; PTMSC 2000).

Sediment Quality

Several more years of monitoring is required to identify trends in sediment chemistry. Chronic effects with long-lasting consequences for the biological community have not been assessed (Llanso et al. 1998).

Industrial Contamination - Further testing is needed to measure dioxin levels at potential source generators statewide to more accurately assess actual dioxin emission levels. The importance of obtaining additional data on hog-fuel burning sources is ranked high due to the combination of little data, high number of hog-fuel burning facilities and the high variability in factors that lead to dioxin formation and control. Port Townsend Paper Mill is not one of the few for which dioxin load data is available (Llanso et al 1998).
 

3. NEARSHORE HABITATS

CHARACTERIZATION OF THE RESOURCE

Marine and estuarine waters consist of varying localities and environmental conditions referred to as "habitats" in which specifically adapted organisms reproduce, feed and take shelter. Seasonal variation in primary and secondary productivity, wave energy, and variations in animal life-history stages combine to determine the ability of any one habitat to support a given species at any one time.

Photosynthetic production of new plant material is the first link in plant and animal food chains. Primary producers such as diatoms and phytoplankton support juvenile salmon, who prey on small copepods feeding on the diatoms and microbial colonizers associated with microalgae and detritis (Cordell 1986, D'Amours 1987). Light provides the essential energy that drives plant photosynthesis. A plant's ability to utilize light energy is defined by the structure and pigments of its chloroplasts, which are the sites of photosynthetic reactions (Lobban et al.1985). Light is the most important factor affecting plants. The photosynthetic process converts solar energy into photochemical energy through an oxidation-reduction reaction. Basically, in green plant photosynthesis, CO₂, H₂0, and light energy are the reactants and O₂ and CH₂O are the products. The photochemical process of light trapping increases linearly as irradiance increases until a maximum photosynthetic "saturated" rate is reached for a given plant. At that saturation point, increased irradiance no longer results in increased production. Essentially, growth takes place when enough light energy is received and stored to support the initial electron transfers of the reaction process, the creation of new plant tissue and the subsequent cellular respiration process that uses O₂ and releases CO₂. During spring and summer, nutrients imported to Puget Sound through watersheds and oceanic upwellings and the increased light availability due to the combination of the seasonal angle of the sun to the earth and low tides during daylight hours sets the stage for peak levels of primary productivity. This primary productivity is further enhanced by the prior mixing of waters during winter storms and the lack of growth and subsequent respiration processes occurring over the winter season (Simenstad et al 1999). It is this primary production, particularly in the shallow nearshore habitats that supports large numbers of juvenile fish and shellfish in estuarine and marine habitats.

Shallow nearshore marine habitats provide important passage for juvenile fish, larvae, and ocean water. Protecting and conserving these important habitats is key to protecting the future of important fish and shellfish stocks and species diversity. In Washington, habitat loss has been identified as the most serious threat to the marine ecosystems of Puget Sound and the Northwest Straits. The British Columbia/Washington Marine Science Panel (1994) assigned nearshore habitat this priority based upon: 1) the importance of such habitat for the survival of valued species; 2) the region's current and projected rapid increase in human population and its projected effects on natural habitats, and 3) the known irreversibility of habitat alteration and loss. Due to their proximity to urban development and their limited areal extent, nearshore marine habitats are particularly vulnerable to loss and degradation (Norris 1991a; Doty and Landry 1990). The importance of shallow nearshore vegetated habitat has been well documented. Habitats previously assumed to be unproductive are now recognized as important nurseries (Bennett 1989). The limited extent of a given habitat utilized during a particular life stage is theorized to cause a "bottleneck" in the ability of the species to produce viable adult populations (Wahle and Steneck 1991). Alarming declines in plant and animal populations in Washington's inland marine waters (Wright 1999) have magnified the need to identify and avoid stressors to the nearshore fauna. Fish populations suffering from significant anthropogenic stresses in need of special consideration for protection include Pacific salmon, Pacific herring, Pacific cod, walleye pollock, Pacific hake, and three species of demersal rockfish (Wilson et al. 1994, West, 1997). Other nearshore fishes, critical to these species are forage fish such as herring, sand lance, and surf smelt. At some point in their juvenile rearing stage, each of these species rely on nearshore vegetated habitat to meet critical rearing needs in a habitat rich in both prey resources and shelter.

Areas from above the highest tideline and out as far as 15 m MLLW are important to the recruitment and survival of some of the region's most important fish and shellfish. Above the tideline of vegetated habitat, in the area between higher and lower high tidelines, sandy beaches provide spawning grounds for important forage fish, such as sand lance and surf smelt. The marine riparian vegetation above the highest high tide line plays a significant role in determining egg survival during periods of high temperatures. Intertidal areas between mean high tide and lower low tides are used by herring and lingcod for spawning. Pacific herring and sand lance are principal food organisms for many recreationally and commercially important fish species (Simenstad et al.1979a,1979b). Herring have been found to comprise the following diet percentages of specific fish species: Pacific cod (42%), whiting (32%), lingcod (71%), halibut (53%), coho (58%) and chinook (58%). (Environment Canada 1994). Mean high tide areas are also important nursery areas for a variety of juvenile fish including salmonids, cod, herring, sand lance, surf smelt, sole and pollock. In the lower tide areas from mean low tide to the lower low tide and out as far as -40 feet are important nursery areas for a variety of juveniles. These include salmon, lingcod, tomcod, hake, walleye pollock, herring, a variety of rockfish, and shellfish (Simenstad et al 1979a; Matthews 1989; Palsson 2000; Haldorson and Richards 1987). Substrate type, depth, light, and wave energy are physical factors determining the nature of the biological assemblages found in these environments. Water quality also influences the nature of these habitats with the presence of contaminants and excess nutrients degrading the habitat's ability to support important plant and animal species.

HABITAT TYPES

Rocky-Bottom Habitats

Rocky bottom habitat is found in a variety of locations throughout the Jefferson County MRC area. Beaches on the west side at the northern end of Discovery Bay and along the Strait of Juan de Fuca between Point Wilson and McCurdy Point are composed of mixed cobble, small boulders and gravel. Similarly, boulder and cobble piles left by receding glaciers in the straits provide subtidal rocky reef habitat at Smith Island and Partridge Bank just north of Admiralty Inlet.

Substrate - These rocky-bottom habitats support kelp and other vegetation that require hard surfaces for holdfasts and rock surface area for benthic microalgae. These hard surfaces also provide attachment sites for barnacles, mussels, chitons, tube worms, seastars, and anemones and crevices for small crustaceans and annelids (Shaffer 1999). Rocky reef habitat north of Port Ludlow near Mats Mats Bay, a lone stack of boulders and a sunken vessel in Discovery Bay support documented rockfish populations (Palsson 2000).

Wave Energy - The steep gradient and well-flushed character of rocky outcrops in deep, high energy areas such as the Strait of Juan de Fuca, provide animals in the kelp beds with access to large neritic organisms found in deeper waters. These are the habitats that support adult rockfish, lingcod, kelp greenling, cabezon, salmon and cetaceans. The lower energy cobble rocky-bottom habitats of the intertidal area support a detrital food web. This food web includes those crustaceans brought in with the tide that support sculpins, snailfish, and prickleback fish species.

Vegetation - While the bottom sediments of these rocky habitats are not capable of supporting the large number of infauna found in soft-sediments, many crustaceans such as mysids, crab, epibenthic shrimps, amphipods, isopods and copepods occupy the kelp microhabitats. Kelp and other primary producers provide food supply for these smaller organisms which in turn become prey resources for those fish occupying these habitats while providing shelter for fishes while they feed on these invertebrates. Rocky habitats of Smith Island and Partridge Bank, north of Admiralty Inlet, are some of Washington's largest kelp beds (Mumford 2000). These habitats support lingcod, rockfish, halibut, kelp greenling, cabezone, salmon, and large cetaceans (Palsson 2000).

In the cobble littoral habitats between Point Wilson and McCurdy Point on the Strait of Juan de Fuca, grazers are sustained by the seasonal breakdown of macroalgae and the grazing action of chitons, limpets, sea urchins, and snails. Macroalgae breakdownt release macroalgae from the substrate supporting crab and such fish species as sculpin and snailfish. These habitats are some of the most productive due to both geographic extent in the area and the standing stock of the community which includes both on-the-rock and beneath-rock habitat.

The kelp beds at Smith Island that extend into Jefferson County represent one of the largest kelp beds in the state of Washington (Mumford 2000). A second large kelp bed is located in the Strait of Juan de Fuca and is bisected by the Island and Jefferson County boundary line. Ten years ago rich kelp beds existed on the western side of Protection Island. These kelp beds began gradually disappearing in 1990 and completely disappeared by 1996. Figure 2 depicts kelp changes on Protection Island over time. However, a large, rich eelgrass bed is now located on the northwest side of Protection Island (Bookheim 2000). The disappearance of kelp around Protection Island is an unexplicable mystery at this point in time.

Figure 2. Protection Island Kelp Distribution Changes

Source: Mumford, Tom, DNR, Nearshore Habitat Program

Sand-Eelgrass

Soft-bottom habitats include sand-eelgrass, mud-eelgrass, mud and sand flats, and salt marshes. Sand-eelgrass habitats in northern Puget Sound and the Strait of Juan de Fuca are shallow, semi-enclosed embayments with low-to moderate-energy beaches which allow sand and mixed fine gravel to accumulate and stabilize.

Substrates - These stable substrates support particularly high abundances of benthic and epibenthic crustacean communities for juvenile salmon and demersal fish seeking refuge and prey in eelgrass beds. Eelgrass shoots increase the substrate available for the epiphytic algae and associated fauna, thereby increasing the abundance of prey resources, such as the harpacticoid copepods, tanaids and cumaceans available as prey to juvenile fish (Simenstad et al. 1979a, 1979b).

Wave Energy - Eelgrass beds reduce wave and current action and trap sediments and detritus. Through photosynthetic activity, eelgrass beds have been found to maintain high dissolved oxygen concentrations and minimize fluctuating temperatures (Gayaldo 1999).

Vegetation - Through autumn die back and atrophy of the emergent growth, eelgrass provides great quantities of detrital carbon to the nearshore system. This eelgrass-derived detritus provides energy to both detritivores consuming the vegetation and carnivores consuming animal organisms.

Mud-Eelgrass and Salt Marsh

In terms of community and food web structure, the most complex and highly connected habitats are the mud/eelgrass and associated saltmarsh habitats. These communities contain the highest diversity and abundance of food web linkages ranging from detritivores to carnivores. Much of this increased food web complexity is due to the presence of benthic-feeding shorebirds such as the saderling, longbilled dowitcher, shorebilled dowitcher, yellowlegs, the great blue heron who preys on a number of demersal fishes. Although this habitat supports many of the same species as sand/eelgrass habitat, it provides higher densities of each taxon (Simenstad et al. 1979a).

Substrate - The small fine-sized substrates of mud and eelgrass habitats consist of combined mineral and organic soils transported by streams and open marine waters into protected embayments. The high levels of plant production in adjacent salt marshes and marine waters combined with the material transport and entrainment processes endemic to the area create the fine organic and mineral substrates that support the rich benthic diversity of these habitats.

Vegetation - Vascular marsh plant detritus tends to accumulate and decompose in the mud flats as a result of spring runoff and spring tides. The protected nature of these embayments result in reduced indications of seasonal change in habitat food web structure and diversity (Simenstad et al. 1979a).

STATUS OF THE RESOURCE

Mapping Nearshore Habitats

In 2000, the Washington State Department of Natural Resources (DNR) and the Point No Point Treaty Council each undertook regional mapping efforts using aerial multispectral digital imagery technology to map nearshore habitat specific to the region. These mapping efforts identifed substrate and vegetation types throughout the Jefferson County MRC region through the combination of interpreting aerial multispectral data and correlating it to simultaneous on-the-ground sampling efforts. The data from both mapping efforts will be compatible and are expected to be available by 2001. The WDNR inventory data will be classified by segment according to the following categories: shoreline type, eelgrass/surfgrass - patchy or continuous; kelp (Nereocystis) -patchy or continuous; kelp (Macrocystis)-patchy or continuous; other flora/fauna; segment length (feet); sediment source; sediment abundance; sediment transport direction; stability; natural resources damage assessment classification; energy exposure; oil residence index; supratidal form and material, and intertidal form and material. The primary goal of this mapping program is to catalog shore-zone features for resource management. It is designed to capture key ecological features of the shore-zone. The Point No Point Treaty Council study will complement the WDNR data with identification of specific vegetation and substrates resulting from the intensive groundtruthing effort.

Additional information on net shore drift specific to Jefferson County is found in Johannessen (1992), Net Shore-Drift of San Juan, and Parts of Jefferson, Island and Snohomish Counties, Washington and the USGS Map of Shoreline Coastal Erosion, Sediment Supply and Longshore Transport in the Port Townsend I-1198-E 30- by 60-minute quadrangle. Together these reports map out net shore-drift within the Jefferson County MRC boundaries.

Jim Norris with Marine Resources Consultants has been surveying eelgrass using underwater videography throughout Port Townsend Bay for several years. His reports document eelgrass encircling Port Townsend Bay at subtidal depths varying form 3 ft MLLW to as deep at 38 feet MLLW (Norris1995, 1997, 1998).

Critical habitats from Tala to Kala Point have been comprehensively surveyed, mapped, and identified in terms of drift cell processes, eelgrass presence, marsh habitat, and forage fish and salmonid use. Such documentation has enabled protective shoreline designations pursuant to the local shoreline management planning (Hirschi 1999; Johannessen 1999).

Nearshore habitats are distinguished by important variations in habitat characteristics and the plant and animal assemblages associated with particular habitats. Recent shoreline mapping efforts and scientific analyses use the Natural Heritage Program: Marine and Estuarine Habitat Classification System. This system classifies habitats by the physical components controlling habitat characteristics. Such physical parameters constrain the distributions and interactions of marine plants and animals associated with these habitats. These basic controlling factors are substrate type, wave energy, depth, and salinity. Knowing these physical factors, distinct and recurring plant and animal assemblages associated with each other and a particular physical environment (Dethier 1990) can be predicted. In place of using a salinity-based cutoff, nearshore habitats west of Pt. Wilson and those south of Admiralty Inlet are classified as marine, while habitats south of Admiralty Inlet are considered estuarine. In Appendix B, Table 1 categorizes general marine and estuarine nearshore habitats and identifies plant and animal species commonly associated with those habitats. In Appendix B, Table 2 classifies Jefferson County System and Subsystems based upon DNR survey data (Dethier 1990).

Status Reports

Marsh Areas

Northwest Environmental consultants (1976) prepared a report for the Jefferson County Planning Department describing the location, size, features and ownership of each tidal marsh of Jefferson County. The 13 marshes lying within MRC boundaries between Olele Point and Discovery Bay described in that report are listed in Table 1.

Table 1. Jefferson County MRC Marsh Areas
 

Marsh	Marine/Estuarine Area	Size
Gardiner	Discovery Bay	5.7 acres
Chevy Chase S.	Discovery Bay	2.7 acres
Chevy Chase N.	Discovery Bay	1.5 acres
Beckett Point	Discovery Bay	6.6 acres
Discovery Junction	Discovery Bay	3 marshes
Kala Point	Port Townsend Bay	8.5 acres
Chimacum Creek	Port Townsend Bay	35 acres
Hadlock	Port Townsend Bay	1.3 acres
Oak Bay	Oak Bay	10.3 acres
South Indian Island	Oak Bay	11.1 acres
Olele Point	Oak Bay	2 marshes
Indian Island	Kilisut Harbor
Scow Bay	Kilisut Harbor	7.8 acres
Total Acres		>70 acres

Spartina Invasions - The Washington State Department Agriculture (WSDA) 2000 Spartina Management Plan for the Straits of Juan de Fuca/Pacific Ocean describes the status of spartina invasion in marshes located within the Jefferson County MRC boundaries and the restoration activities planned to counter this invasion. The following activities are planned to restore and protect marshes from spartina invasion.

Kala Point - The largest colony of Spartina anglica at this site is estimated to be 45,000 square feet with many smaller clones in a nearby lagoon. From 1996 Adopt-A-Beach volunteers and WSDA staff have worked with local landowners on treatment to remove the infestation. During this time it has been removed repeatedly and treated with herbicide, but it continues to grow and require additional treatment.

Oak Bay - This Spartina anglica infestation is located on both the east and west sides of Oak Bay. In 1997, the total area of spartina in Oak Bay was one half acre. Between 1996 and 2000, Adopt-A-Beach volunteers and WSDA staff have worked with landowners to treat and extract clones. Treatment has taken the form of mowing and manual removal. Following the 1999 removal, no signs of re-growth have occurred. WSDA staff and Adopt-A-Beach volunteers monitor the site for regrowth. Treatment will occur as necessary.

A marsh owned by Jefferson County on the northwest shore of Oak Bay is in need of restoration due to currents and wave action caused by the dredged channel between Indian Island and the Quimper Peninsula. Wave action deposits large woody debris upon the shore altering the marsh ecosystem (Shaffer 2000).

Scow Bay - In 1996, Adopt-A-Beach volunteers discovered a Spartina anglica infestation located in the south end of Kilisut Harbor. An Infestation size was estimated at 0.02 acres prior to the 1999 treatment. Between 1996 and 2000 WSDA staff and Adopt-A-Beach volunteers have been removing infestations. The site will continue to be monitored with treatment occurring as necessary.

Mats Mats - An infestation of Spartina anglica was discovered in 1996 with the estimated size at 0.02 acres. Between 1996 and 2000 Adopt-A beach volunteers and WSDA staff have been manually removing clones. The site will continue to be monitored with treatment occurring if necessary.

Whalan Point - Spartina altnerniflora was discovered in 1996 on Navy property. 15 to 20 clumps less than two feet in diameter were located between Whalan Point and Crane Point. Approximately 0.02 acres of infestation are estimated at this site. Between 1996 and 2000 the Navy has been working with WSDA to manually remove the infestation. The Navy will continue to survey the site and treat as necessary. Treatment will most likely be a combination of mowing and herbicide spraying.

Fort Flagler - An infestation of two small clones of Spartina anglica was discovered in 1999. WSDA and Adopt-A-Beach continue to monitor this site, manually removing infestations as they occur.

Indian Island - Indian Island has three infestations at sites on the north, east, and south sides of the island. The total size is approximately 0.6 acres. Between 1999 and 2000, WSDA and the Navy have manually removed, mowed and treated with herbicide infestations as they occur. This will continue as necessary.

Discovery Bay - Spartina Infestation has also occurred at the southern end of Discovery Bay.

Chimacum Creek - The Chimacum Creek marsh area is to be re-established and protected by Jefferson Land Trust and the Washington State Department of Fish and Wildlife.

Seaweed Harvesting Report - Levings and Thom (1994) characterize areas with intertidal algae such as seaweeds and kelp, as being highly productive, containing a variety of species of algae that provide refuge and rich prey resources for several species of fish, including salmonids, rockfish, gunnels, greenling and lingcod. Norris et al. (1999) studied seaweed harvest impacts between 1996 and 1998. The study reported an estimated 200-300 recreational seaweed harvesters removed 2,000 to 4,000 pounds of the seaweed Alaria from North Beach County Park on the Strait of Juan de Fuca. In 1996 and 1997, the percent cover of Alaria dropped by 35% from 50% cover to about 15%. Comparison of Alaria recruitment differences between a harvested and unharvested beach showed a sharp decline in the harvested beach, suggesting a dominant harvesting effect.

PROTECTION AND RESTORATION EFFORTS

Chimacum Creek - Chimacum Creek has had significant habitat restoration in the freshwater areas upstream in the Chimacum Valley region to protect stream water quality from farming and livestock impacts. Efforts to remove riprap and fill at the mouth of Chimacum Creek are presently underway by WDFW, ACOE and the North Olympic Salmon Coalition (NOSC). A broad-based coalition of local groups, Wild Olympic Salmon (WOS), North Olympic Salmon Coalition (NOSC), Jefferson County Conservation District (JCCD), Washington State University (WSU), Jefferson Land Trust (JLT), Trout Unlimited (TU), and the Tribes have been partnering over the last two years to protect and restore the marsh and estuarine shorelines of the creek mouth and adjacent shorelines in Port Townsend Bay. Approximately 35 acres of estuarine shoreline and marsh habitat have recently been acquired by WDFW for protection. This is an important salmon migratory corridor for many species including the threatened species Hood Canal summer chum. Coho, steelhead, cutthroat, summer chum and fall chum spawn in Chimacum Creek and sand lance spawn on the beaches immediately adjacent to the creek mouth. Herring spawn on beaches north of the creek and surf smelt spawn further south of the creek mouth. NOSC is presently seeking funding for a prey base study along the shorelines adjacent to the creek mouth.

Salmon Creek - Freshwater habitat restoration is also being pursued by WDFW and NOSC to prevent potential lower creek sedimentation that threatens to destroy the viability of summer chum spawning beds. WDFW is also examining the possibility of improving the habitat conditions in the Salmon Creek subestuary of Discovery Bay (Johnson 2000).

DATA GAPS and RESEARCH NEEDS

Comprehensive identification and mapping of critical nearshore habitats are needed for the areas from Kala Point north through Admiralty Inlet, and west to include Discovery Bay. A comprehensive approach should combine WDFW forage and groundfish survey work, the nearshore mapping products of both WDNR and the Point No Point Tribal Council, and USGS geologic drift cell information to provide comprehensive baseline data for shoreline planning and designation. For trend identification, it will be necessary to insure that replication of these efforts will occur on a minimum cycle of every 5 years.

4. FISH

CHARACTERIZATION OF THE RESOURCE

Washington State inland marine waters, including the Strait of Georgia and the Strait of Juan de Fuca support over 220 fish species. Under the Marine and Estuarine Habitat Classification System for Washington State, which is used by the Washington State Department of Natural Resources, Puget Sound is defined as all of the inland U.S. marine waters east of the Bonilla-Tatoosh Line at Cape flattery and including the U.S. portion of the Strait of Juan de Fuca, U.S. parts of the San Juan Islands, Strait of Georgia, and all of Hood Canal. Puget Sound "proper" is defined as east of Deception Pass, south and east of Admiralty Head and south of Point Wilson on the Quimper Peninsula (Dethier 1990). The northern and southern regions of these inland waters are both geographically and oceanographically distinct. The narrow passage of Deception Pass and the Admiralty Inlet sill separates North Puget Sound from South Puget Sound. North Puget Sound receives strong storm and ocean influences and contains abundant rocky reef habitat. South Puget Sound has more freshwater influence, is more protected in nature, and contains less rocky reef habitat. Water circulation and entrainment of pelagic larvae have a determining effect on the distribution of fishes and shellfish. It is believed that the unique geographic and oceanographic conditions determining water movement and circulation patterns of this region limit gene flow between marine fish populations of the same species (Wright 1999). Similarly, the existence of three separate bodies of water in north Puget Sound (i.e. the Strait of Juan de Fuca, Strait of Georgia and San Juan Archipelago) and the fjord bathymetry of south Puget Sound likely contribute to the gene flow barrier between these regions. This notion of a gene flow barrier is supported by genetic studies of closely-related rockfish species showing significant differences between fish samples taken on opposite sides of the sills at Deception Pass and Admiralty Inlet (Seeb 1986;Wright 1999).

Under the influences of tide, wind and ocean-current-driven convergent zones, detached intertidal and subtidal vegetation form floating mats that move into open water pelagic systems. These floating mats provide cover for small fish along with high densities of planktonic organisms associated with the vegetation (Gorelova and Fedoryako1986). Such dislodged nearshore vegetation provides a link between pelagic and nearshore systems by providing a transportation corridor in the form of refuge and prey resources for small fish settling into or exiting from the nearshore environment. Small fish can use these mats for cover and food as they move under them to new habitats. This nearshore and pelagic mix creates a unique habitat offering components of both the nearshore vegetated habitats and open water pelagic systems. Depending on the season, such vegetation mats have been shown to provide higher abundances of species diversity and richness than is usually found in open water systems. In this way, the mats act as nutrient, larvae, juvenile fish and pollutant transportation systems between nearshore and benthic habitats (Johnson and Richardson 1977, Kulczycki et al. 1981, Kingsford and Choat 1985, Shanks 1987, Kingsford, 1992, J.A. Shaffer 1995). Such drift habitat may be a critical resource for many fish species in Washington coastal waters such as juvenile chum, pink, chinook and coho salmon, surf smelt, Pacific herring, and northern anchovy (Simenstad et al. 1991).

In June, 1999, in response to a petition by Sam Wright (1999), the National Marine Fisheries Service agreed to conduct a year-long biological "status review" of seven species of fish in Puget Sound in order to determine if protection is warranted under the Endangered Species Act (ESA). The seven Puget Sound populations are Pacific herring, Pacific cod, Pacific hake, walleye pollock and brown, copper and quillback rockfish. This represents the largest number the federal agency has ever been asked to consider to date under the federal species-protection law. Table 2 lists those marine fishes currently under biological review for a listing determination.

Table 2: Puget Sound Marine Fishes Currently Under ESA Biological Review

Marine Fish Species

Pacific cod

walleye pollock

Pacific hake

Pacific herring

brown rockfish

copper rockfish

quillback rockfish

In addition to the above proposed listing of marine fish species in Wright's 1999 petition, two populations of Pacific Salmon are presently listed as "threatened" under the Endangered Species Act (ESA). These species are the Hood Canal summer chum and the Puget Sound chinook. The Evolutionarily Significant Unit (ESU) for a given population are prescribed geographically by the area specific to that population's spawning and early rearing habitat that has helped determine their genetic heritage. The Hood Canal summer chum ESU includes all summer chum populations in Hood Canal, all Puget Sound waters between Hood Canal and Admiralty Inlet, and west along the shores of the Strait of Juan de Fuca, including both Discovery and Sequim Bays (NOAA 1997). The Puget Sound chinook ESU includes all chinook runs in the entire Puget Sound basin northwest to the Elwha River and northeast to the North Fork of the Nooksack River (NOAA 1998).

With the exception of limited stream-specific variations, all native Puget Sound chinook are classified as ocean-type chinook that have evolved for early outmigration from their natal freshwater streams to utilize Puget Sound estuarine habitat for juvenile rearing (Myers et al. 1998). These populations also share a commonality in their coastally-oriented ocean migration patterns. In contrast, stream-type chinook in larger rivers, such as the Columbia River, are likely to rear in their respective streams and outmigrate as yearlings with their ocean migration taking place far off-shore. Such genetically transferred biologic adaptation to the geomorphology of their specific regions determines their migration timing and patterns. These shared traits and behavioral patterns across runs in a given region define a given ESU (Myers et al.1998).

Forage Fish

Forage fish, also known as baitfish, include herring, surf smelt, eulachon (Columbia River smelt) anchovy, and sand lance. They are small schooling fish that are important prey resources for commercially and recreationally harvested fish species, such as salmonids and groundfish. Herring have been found to comprise the following diet percentages of specific fish species: Pacific cod (42%), whiting (32%), lingcod (71%), halibut (53%), coho (58%) and chinook (58%) (Environment Canada 1994). On average, 35 % of juvenile salmon diets are comprised of sand lance). They are particularly important to juvenile chinook, with 60% of chinook diet compositions found to be sand lance. Similarly, juvenile coho and sockeye salmon diets were found to be composed of 19% and 53% juvenile sand lance, respectively (WDFW 2000). Forage fish are also important prey for marine seabirds and mammals. Their importance to the marine ecosystem, coupled with their susceptibility to commercial and recreational fisheries during spawning aggregations, and the lack of management and biological information concerning their abundance, mortality rates, and age composition, requires a precautionary ecosystem management approach to protect them from significant population declines.

Surf smelt (Hypomesus pretiousus) - Surf smelt spawn at the highest tide lines at high slack tide near the water's edge, on coarse sand or pea gravel. Egg development rate is temperature dependent, with marine riparian vegetation serving to maintain lower temperatures during high temperature periods. The smelt life-span is thought to be at most 5 years in length. The adults feed primarily on planktonic organisms but their movements between spawning seasons are basically unknown. They are known, however, to be a significant part of the Puget Sound food web for larger predators. Recent surveys document 205 miles of surf smelt spawning habitat in Puget Sound. Inside Puget Sound, they spawn at the high-high water line. While on the coast, they spawn at lower tidal elevations corresponding to accessibility to fine gravel substrates. Spawning in northern Puget Sound occurs year-round, spawning in central and southern Puget Sound occurs in fall and winter, while coast and straits spawning occurs in summer months. As spawning typically occurs in coarse sand and pea gravel, this suggests that substrate is the primary factor in spawning site selection. The limited extent of surf smelt spawning grounds makes them quite vulnerable to shoreline development and construction activities with some spawning grounds being mere remnants of their historical extent (Penttila 2000). Their spawning grounds have been mapped and are protected by state law. Surf smelt spawning beaches in Eastern Jefferson County, within the Northwest Straits area, include the shorelines of Port Ludlow Bay, Hadlock, Port Townsend Bay, Kilisut Harbor, and Discovery Bay. Figure 3 maps surf smelt in the Puget Sound region (Penttila 2000, WDFW 2000).

Figure 3. Surf Smelt Distribution in the Puget Sound Region

(Source: WDFW 2000)

Sand lance (Ammodytes hexapterus) - Sand lance spawning occurs in the upper intertidal on sand and sandy gravel beach material, at high tide. The eggs are coated with sand grains that may serve to assist in moisture retention when exposed during low tides. In Puget Sound, the spawning season is November 1 through February 15. After hatching, larvae and young-of-the-year rear in bays and nearshore waters. Adult movement and age structure are currently unknown. They feed in open water in daylight and burrow into the bottom substrate at night to avoid predation. They are a significant food source of many economically important resources in Washington such as juvenile salmon. It has been found that 35% of juvenile salmon diets are known to be sand lance. They are particularly important to juvenile chinook, with 60% of the juvenile chinook diet represented by sand lance. Their habit of spawning in upper intertidal zones of protected sand and gravel beaches makes them particularly vulnerable to the cumulative effects of shoreline development.

Sand lance spawning beaches have been identified in Kilisut Harbor, Irondale, Hadlock, south and west sides of Indian Island, south and east sides of Marrowstone Island, Port Ludlow, Oak Bay, along the shorelines between Kala Point and Glen Cove, along the Port of Port Townsend beach above the derelict transfer span structure, along the Fort Worden shoreline in Port Townsend Bay and throughout Discovery Bay, including the southern Discovery Junction area (Penttila 2000). Port Townsend provides a rich opportunity to observe the full variety of sand lance life history phases, from spawning along shoreline beaches and juvenile use of nearshore habitat to their adult pelagic movements in large schools where they attract clusters of avian and fish predators (Penttila 2000). Their spawning habitat is protected by the state law. See Figure 4 WDFW mapping of sand lance spawning beaches in the Puget Sound region (Penttila 2000; WDFW 2000).

Figure 4. Sand lance distribution in the Puget Sound Region

(Source: WDFW 2000)

Pacific herring (Clupea harenus pallasi) - Pacific herring are found to be the predominant species in Northern Puget Sound's neritic fish assemblage (Fresh 1979), utilize nearshore habitats for spawning and juvenile rearing. Typically spawning occurs in early spring from January through early April; the female deposits eggs on nearshore vegetation, such as the native eelgrass and the red alga Gracilariopsis, between 0 and -40 feet in tidal elevation (Penttila 2000). Some stocks migrate annually from these inshore spawning grounds to open ocean feedings areas. Studies in northern Puget Sound (Simenstad et al. 1979a) have found juvenile Pacific herring to primarily feed on planktonic organisms with herring in turn serving as an important food source for many marine organisms. Annually, it is estimated that 50-70% of adult herring fall to predation.

The Discovery Bay stock, historically one of the larger stocks in Washington, is currently at a critically low abundance level. The reason for this is unknown at this time. There appears to be no fishery interception or easily recognized habitat degradation, yet they have suffered a serious decline from over 3000 tons in 1980 and 1981 to a run size of zero in 1998 (Penttila 2000). Discovery Bay spawning grounds occur along both shorelines of the southern half of Discovery Bay. The prespawner holding grounds extend from just south of Protection Island in the Strait of Juan de Fuca to the middle of Discovery Bay. The other Jefferson County stock in the MRC region is the Kilisut Harbor stock. This is a small Puget Sound stock with most spawning occurring inside Kilisut Harbor. Spawning also occurs from the mouth of Chimacum Creek north to Glen Cove with the adult prespawner holding areas being in Port townsend Bay. Data on this stock are insufficient to establish trends over the past 5 years (Lemberg et al. 1997).
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Figure 5. Herring distribution in the Puget Sound Reigon

(Source: WDFW)

Groundfish

Groundfish, also known as bottomfish, are legally defined as food fishes. They spend their lives near or on the bottom. Eighty-six species recorded in Puget Sound fall under the legal definition of bottomfish, with 36 of these species commonly occurring in recreational or commercial fisheries. Many of these species have been suffering serious declines since the early 1980's. Important Puget Sound groundfish species, stock status, fishery impacts, and trends are listed in Table 3. Only 28 of these stocks have information sufficient to determine stock status and trends. Thirteen of these 28 stocks have been found to be in decline while eight are increasing (Palsson et al. 1997).

Table 3. Important Puget Sound Bottomfish/Groundfish
 

Species	North Sound	North Sound Stock Status
Spiny dogfish	depressed	average
Skates	above average	unknown
Spotted ratfish	unkown	unknown
Pacific cod	depressed	critical
Walleye pollock	critical	critical
Pacific whiting (hake)	depressed	critical
Rockfishes	depressed	depressed
Sablefish (black cod)	above average	unknown
Greenlings	unkown	unknown
Lingcod	depressed	above average
Sculpins	unknown	unknown
Pacific halibut	above average	above average
Rock sole	depressed	unknown
Dover sole	above average	unknown
English sole	above average	unknown
Sand sole	above average	unknown
Surfperches	unknown	average
Starry flounder	above average	unkown

Source: 2000 Puget Sound Update. PSWQAT.

Pacific cod ( Gadus macrocephalus) - Cod live near the bottom over soft sediments. They feed on sand lance, herring, pollock, sculpins, flatfishes and invertebrates such as euphausids, crabs and shrimp (Albers and Anderson 1985, Jewett 1978, Blackburn 1986, and Westrheim and Harling 1983). As adults, they are a demersal fish, found primarily at depths from 50 to 200m (Matthews 1987). They spawn in the winter and following spawning migrate to feed in deeper, cooler waters. Their spawning occurs in shallow waters during the winter (Westrheim and Tagart 1984). They are broadcast spawners with the largest females producing millions of eggs. Following spawning, the eggs sink to the sea floor and adhere to substrate particles. Upon hatching, larvae 3-4mm in length rise to a depth of 15-30 m in the water column. After several months in the water column, they metamorphose into their juvenile form. In late summer, the juveniles settle to shallow sand-eelgrass habitats where they find shelter and rich abundances of prey resources in the form of copepods, amphipods and mysids.

In Puget Sound, cod are found to concentrate in shallow embayments such as Port Townsend Bay and Agate Passage during the winter but disperse to deeper waters during the remainder of the year (Walters 1984, Bargmann 1980). Stomach content analyses have demonstrated that Pacific herring are main prey items (Palsson 1990). Walters (1984) found that as juveniles, Pacific cod hatched during winter in Port Townsend Bay, remained in the shallow areas until June, and then left the shallow water in June. Westrheim (1983) distinguished four cod stocks in inland marine waters of British Columbia consisting of three resident stocks and one highly migratory stock with documented migration and straying between British Columbia and Washington waters. Water temperature and the presence or absence of herring have been found to affect cod recruitment and abundance in British Columbia (Palsson 1990). Walters et al. (1986) found when herring abundances are low, that cod are likely to move to other feeding grounds or suffer from reduced egg production due to the lack of prey resources.

Karp and Miller (1977) found cod in high abundance in Port Townsend Bay, particularly during their December to March spawning period. During the remainder of the year the stock was distributed over a wider area with reduced densities in the bay. Observations and reports indicated that the Port Townsend population likely spawned in the vicinity of Whalan Point on Indian Island. In 1977, the observed growth rates of the Port Townsend Pacific cod were high. This is expected of a species near the southern limit of its range. The very high abundance of eggs and larvae at the Port Townsend site indicated that the harbor was once an important rearing area. Trynet catches indicated the presence of a substantial Pacific cod nursery located in the northern portion of Kilisut Harbor. It was concluded that the shallow inshore waters north and south of Whalan Point could be important as nursery grounds and could be impacted by the Navy's ammunition dock proposed for Whalan Point. Since the survival of juveniles is often a significant factor in determining recruitment success, these areas could be vitally important to sustaining the Port Townsend Bay Pacific cod fisheries. The large catch of one-year-old pre-recruit Pacific cod provided substantial support for the argument that this population spends a substantial part of its early life in the bay itself (Karp and Miller 1977). During 1977-78, the Navy constructed a two-berth ammunition-loading pier extending 300 m into Port Townsend Bay from Whalan Point.

Since the 1920s, a trawl fishery for Pacific cod existed in this area. In February 1975, a set net fishery was also established in Port Townsend. Karp and Miller (1977) found the cod caught by the trawl method to be relatively small, while the set net fishery in Port Townsend Bay consistently landed cod of greater average length than the trawl fishery. Karp (1977) interpreted this to reflect that only a limited proportion of the spawning population, two and three year olds, were available to the trawl fishery while the set net fishery was taking four and five year olds. While the older fish seemed unavailable to the trawl fishery either by avoidance or location, they were not able to escape the set net fishery.

By 1991, Pacific cod in Port Townsend Bay disappeared. Despite prohibitions imposed on cod fishing in Port Townsend Bay listed in Table 5, the populations have not returned (Palsson 2000). This lack of return is likely due to climate change producing a warmer temperature regime. The presence of Pacific cod in Port Townsend Bay is particularly susceptible to shifts to warmer temperature regimes as Port Townsend represents their southernmost boundary (Palsson 2000). See Figure 13 for WDFW 2000 trawl survey results identifying the presence of cod in the Port Townsend and eastern Jefferson County area (Palsson 2000).

Pacific hake and walleye pollock (Merluccius productus and Theragra chalcogramma - Hake and pollock migrate to inshore, shallow habitats for their first year and move back to deeper water in their second year. As adults, hake and pollock are midwater schooling codfish with small resident populations in Puget Sound. Born as free-swimming pelagic larvae and after metamorphosing to juveniles, they settle to eelgrass and kelp beds. Like salmon, nearshore nursery habitats provide prey and refugia while they undergo extensive physiologic changes and become oriented to solid substrates. Their final adult habitat is in the water column above or on sand and mud basins.

English sole (Parophrys vetulus) - English sole are a common offshore species that utilize a variety of nearshore habitats as juveniles. Miller et. al (1976) found juveniles in gravel, sand-eelgrass and mud-eelgrass habitats. Larvae were found in nearshore habitats between March and May and juveniles were found throughout the year in eelgrass habitats feeding on annelids. English sole spawn offshore between September and April (Kruse and Tyler 1983). Following a pelagic early larvae stage, they move into the benthos of coastal and estuarine areas where they assume a demersal existence for the remainder of their lives (Tasto 1983; Stevens and Armstrong 1984; Krygier and Pearcy 1986; Boehlert and Mundy 1987). English sole larvae of 15mm in length settle to the substrate and at times burrow into it. Gunderson et al. (1990) found that as the fish reached 55m in length, the majority were found in estuarine waters. Emigration from the estuaries were found to begin at 75-80mm with fish greater than 125mm having emigrated from the estuaries. Gunderson et al. (1990) found this migration in and out of estuaries to be length-dependent. The estuaries provide juveniles with prey resources and refuge. The disproportionately high settlement in estuaries and larval distribution patterns (Reilly 1983; Boehlert and Mundy 1987; Jamieson et. al.1989) suggest an active migration or directed transport to estuarine areas for settlement. This finding is consistent with a wide variety of fish and crustacean studies describing the importance of specific larval behavior patterns and interactions with physical processes that assure recruitment to estuaries (Gunderson et al. 1990; Rothlisberg 1982; Rothlisberg et al. 1983; Epifano et al. 1984; Johnson et al. 1984; Sulkin and Epifano et al 1986; Boehlert and Mundy 1988; Epifanio 1988; Shenker 1988).

Gunderson et al (1990) states that clearly prey availability is of major significance in evaluating the advantages of an estuarine existence. In studies off the Oregon Coast, English sole 17-35mm fed primarily on polychaete palps, juvenile bivalves, and harpactiocid copepods. Juveniles 35-82 mm fed on the larger amphipods and cumaceans (Hogue and Carey 1982). Toole (1980) found English sole in Humboldt Bay estuary to feed almost exclusively on harpacticoid copepods and the diet of 66-102mm sole to be dominated by polychaetes. Buechner et al (1981) found the diet of English sole in Grays Harbor to be dominated by harpacticoid copepods and gammarid amphipods in April through August and polychaetes predominating in October.

Rockfish (sebastesspp) - Rockfish inhabit rocky reef habitats as adults but use the nearshore habitat to meet juvenile rearing needs. As adults, they do not venture outside of 50m² from their preferred habitat. Born around April as free-swiming pelagic larvae, rockfish spend four months in open water (DeLacey et al. 1964). During their first year, juveniles settle into shallow habitats vegetated by bull kelp, macroalgae and eelgrass to meet critical juvenile rearing needs (Miller et al 1976, 1978; Phillips, 1984; Stober and Chew, 1984; Haldorson and Richards, 1987; Matthews, 1990; Norris 1991a). These nearshore habitats provide juvenile rockfish shelter from predation and increased access to prey resources. Juvenile survival is likely dependent upon the availability of suitable refuge habitat provided by nearshore environments (Norris 1991a). In addition to vegetated nearshore habitats, the habitats most utilized by juvenile rockfish are gravel habitats providing benthic crustacean prey resources (Miller et al.1975). Copper, quillback and brown rockfish generally eat small fish and epibenthic prey with their seasonal distribution likely reflecting prey presence. Summer feeding plays an important role in providing food for storing fat reserves for winter maintenance. Even though rockfish are a vivaparous species reproducing pelagically, pregnant rockfish make use of rocky reef and vegetated habitats to provide protection during the spring parturition period. It is likely that it is the availability of juvenile habitat and not local adult density that predicts local recruitment success. These early nursery habitats likely determine fish stock density through prey resource access and protection from mortality. Limited availability of such habitat is thought to impose a demographic bottleneck on stock recruitment (Wahle and Steneck 1991; West et al. 1995). The seasonal variation in vegetated habit is reflected in dramatic density differences (Buckley, R.M.1997). Matthews (1989) found the highest fish densities in low-relief rocky reef and sand-eelgrass habitats occurring in summer with fish densities declining in these habitats consistent with vegetation die-back. This is likely due to the lack of places for fish to hide in these habitats when vegetation disappears (Matthews 1989; Quast 1968; Stephens et al. 1984; Ebeling and Laur 1988). While winter fish densities in high-relief habitat is likely correlated to the presence of holes and crevices for fish to hide in, temperature also affects juvenile rockfish growth during their first year. Warmer temperatures, such as those found in the nearshore areas, can produce higher growth rates by possibly increasing fish food assimilation efficiency (Buckley, 1997;Love et al. 1991). Some juvenile rockfish utilize drift habitat formed by macrophytes and seagrass for prey resources and protection from predation while moving between pelagic and nearshore habitat (Buckley 1997; Bohlert 1977).

As adults, rockfish require complex, high relief substrate such as rocky or artificial reefs, slopes, pinnacles, pilings or submerged debris. Their home range is small (approximately 30-50 m² ) with little migration once they find suitable adult habitat. This site and habitat specificity makes them particularly susceptible to rapid overfishing. This small home range and their long life span of 60-90 years, coupled with late maturation results in a long recovery period following over-harvest.

Lingcod (Ophiodon elongatus) - Lingcod typically have a relatively small home range. They spawn between December and March laying eggs in rocky crevices in shallow areas with strong water motion. Eggs are then fertilized and the nests are vigorously defended by the males. After dispersing from their nests, larvae spend two months in pelagic habitast as surface-oriented larvae. In late spring-early summer, juveniles move to benthic habitats, settling in shallow water vegetated habitats (Buckley et al. 1984; Cass et al. 1990; West 1997). It is likely that juveniles use nearshore habitats for shelter and feeding. In their first fall season, juveniles move to flat, featureless bottoms where they will spend a year or two growing to a size large enough to avoid predation by other reef-dwelling species (i.e. rockfish, cabezon, larger lingcod) and move to their adult rocky reef habitat.

In studies of demersal fish populations in Port Townsend Bay, Norris caught only three juvenile cod and no adult Pacific cod in the 1991 study trawls and only one juvenile cod and no adults in the 1992 study (Norris 1991b,1992). In general, catches of the ten most abundant species were significantly lower in 1992 than 1991. Norris' 1991, 1992, and 1997 abundance surveys report a significant difference in species compositions in the northern and southern portions of Port Townsend Bay. He attributes these differences to oceanographic and fauna differences between the two regions with considerable upwelling with flood tides occurring in the northern region of the bay. Table 4 reports Norris' 1991 and 1992 trawl results.

Table 4. Port Townsend Bay Demersal Fish Abundance-10 most Abundant Species 1991- 1992
 

Trawl Year	Pac. tomcod juv	Snake prickleback	Pac. herring	Shiner perch	blackbelly eelpout	Eng. sole	Flathead sole	Spotted ratfish	Pac. tomcod	shortfin eelpout
1991	1,403,655	100,964	55,505	44,436	39,588	36,544	32,894	26,994	24,156	17,874
1992	456,832	163,762	93,674	88,518	57,329	47,466	43,712	33,392	29,374	26,494

Source: Norris Abundance Estimates for Demersal Fish Populations in Port Townsend Bay, WA 1991;1992

Catch records for harvested marine fishes show substantial decline in recent years, with concomitant increases in fishing activities (Schmitt et al. 1994). To what degree harvest has contributed to the decreased abundance of some of these species is unknown. However, the life-history strategies of these fish make them particularly susceptible to harvest impacts to fish size, stock recruitment, and abundance. West (1997) describes "growth" overfishing as ultimately having the impact of reducing the average size of fish in a given population. This occurs by chronically harvesting the largest fish. This, in turn, profoundly effects fecundity and egg quality as smaller, younger marine fish tend to produce fewer larvae. Fecundity has been found to increase exponentially with increased size in species such as rockfish and lingcod. Therefore, limiting the size of the reproducing fish is likely to limit its fecundity or reproduction capacity.

Management

Since 1970, those major regulatory changes in commercial and recreational fisheries listed in Table 5 have impacted fishery effort trends. Following the Boldt decision and its salmon harvesting reallocation that designated 50% of the region's salmon harvest to native salmon fisheries, non-native fishers turned to increased fishing of groundfish. The detrimental effects this would impose on groundfish populations were basically unknown at that time (Palsson 2000). Since that time and in the face of declining runs, resource managers have imposed a variety of limitations on groundfish harvest. In North Sound, trawling increased from 10,000 hours to as high as 19,000 hours from the late 1970's through the1980's then declined to less than 12,000 hours since that time. In South Sound, trawling was relatively constant between 1970 to 1989 at 4,000 hours per year. From 1989 to 1993, bottom trawling was restricted to Admiralty Inlet, since 1994. Since 1994 it has been prohibited in Admiralty Inlet and the straits (Palsson et al. 1997).

Table 5. Groundfish Harvest Management
 

Year	Regulation
1978	Lingcod moratorium in South Sound south of Admiralty Inlet
1982	4.5 inch mesh size requirement for bottom trawls.
1983	Lingcod moratorium ends. Six week lingcod season in South Sound. Institution of ten fish bag limit of rockfish for recreational anglers in North Sound, five fish in South Sound. Twelve inch minimum commercial landing size for English sole. Fourteen inch minimum commercial landing size for starry flounder.
1984	Permanent closure in San Juans to bottomfish jig and troll gears.
1985	Limited entry for trawlers fishing for Pacific whiting in areas of South Sound. Depth and area restrictions for the bottom trawl fishery.
1987	Closure of the commercial fishery for Pacific cod.
1989	Bottom trawling south of Admiralty Inlet banned by Washington Legislature.
1991	Agate Passage winter closure to protect Pacific cod spawning, daily bag limit reduced from fifteen fish to two fish. Directed commercial fisheries for rockfish and lingcod prohibited by banning roller gear on trawls. Winter closure of bottom trawl fishery near Port Townsend and Protection Island.
1992	Further lingcod restrictions including reduced season from seven months to six weeks in North Sound and minimum/maximum size limits. Reduction of daily bag limit for walleye pollock form fifteen fish to five fish. Ban on bottomfish jig and troll gears east of Sekiu enacted.
1994	Rockfish daily bag limit reduced to five rockfish in North Sound and three in South Sound. Bottom trawling prohibited in Admiralty Inlet, the eastern Strait of Juan de Fuca and the San Juan Archipelago.

Source: Palsson, W., J.C. Hoeman, G.G. Bargmann and D.E. Day. 1997. 1995 Status of Puget Sound Bottomfish (revised)

Salmon

Pacific salmon (Oncorhynchus spp.) depend upon a wide range of habitats throughout their life cycle. Eastern Jefferson County has at least sixteen salmon-bearing streams draining into the marine and estuarine waters in Hood Canal, Oak Bay, Port Ludlow Bay, and Discovery Bay. Table 6 identifies salmonid use of these natal streams. Seven of these streams support Hood Canal summer chum and four support Puget Sound ocean-type chinook. These two species return in September and October with small fry emerging from the gravels in early spring for spring and summer outmigration to the open ocean. All streams support cutthroat trout and at least nine streams support steelhead. The summer chum, chinook, and pinks return to their natal streams to spawn between September and October. The coho and fall chum return between October and January. Upon emergence from the gravel redds of their natal streams, there is wide variation among species on the extent of their use of various freshwater and saltwater habitats. With some variations, the coho species in this region tend to rear in their natal stream for one to two years, while the chum and pinks salmon outmigrate very soon following emergence from their natal stream gravels at sizes as small as of 25-35+mm, the ocean-type chinook from Hood Canal drainages outmigrate at 60-90mm. The summer chum outmigrate within days and others, such as fall chum and chinook, within weeks. This spring and summer outmigration places them in the Puget Sound estuary during its peak period of primary production. The following table identifies salmon populations supported by Eastern Jefferson County streams draining into Hood Canal, Port Ludlow, Port Townsend, and Discovery Bays.

Table 6. Eastern Jefferson County Salmon Populations
 

Stream	Chinook	Summer Chum	Fall Chum	Coho	Pinks	Steelhead	Cutthroat
Big Quil	X	X	X	X	X	X	X
Little Quil	X	x
Chimacum		X	X	X		X	X
Contractor's				X			X
Dosewallips	X	X	X		X	X	X
Duckabush	X	X	X		X	X	X
Eagle Creek	unk	unk	unk	unk	unk	unk	unk
Jackson			X				X
Ludlow			X	X			X
Salmon		X		X		X	X
Shine							X
Snow		X		X		X	X
Spencer			X				X
Tarboo			X	X		X	X
Thorndyke			X	X			X
Wolcott			X				X

Sources: WDF & WWTT 1992; Parametrix 2000; Correa 2000)

Habitat - Primary production fuels the juvenile salmonid food web. In marine and estuarine waters, juveniles prey upon the small copepods (i.e. secondary producers) that feed upon diatoms and other microbial colonizers associated with microalgae and detritus (Cordell 1986, D'Amours 1987). Studying migrating juvenile chum in Hood Canal, Simenstad (1980) found chum to selectively prey on the harpacticoid copepods found in very high quantities in eelgrass beds. Study findings suggest links between the availability of harpacticoid crops, migration speed, and fish size. Smaller cr