The estuarine waters of the sanctuary are rated “fair/poor” and a trend is “undetermined.” Elkhorn Slough and adjacent water bodies, including Moro Coho Slough, Moss Landing Harbor, Salinas River Lagoon, and Old Salinas River Estuary, are impaired by pesticides and pathogens (see Table 1, in Nearshore/Water quality section, Question 1; SWRCB 2006).

Bioaccumulation studies that measure the amount of chemicals being absorbed by animal tissues have detected high levels of DDT (and its metabolites) and other pesticides in both resident and transplanted bivalves in Elkhorn Slough (Phillips et al. 2002). NOAA’s National Status and Trends’ Mussel Watch program indicates that Elkhorn Slough has levels of cadmium, DDTs, and dieldrins that are high relative to other national sites (Kimbrough 2008).

Toxicity tests demonstrate that in some instances, contaminants in Elkhorn Slough have short-term impacts on individual organisms. Predation on toxic prey has implications for long-term effects on community structure and organisms at higher levels in the food chain (Phillips et al. 2002). Water collected from Tembladero Slough has been shown to cause toxicity to small crustaceans, attributed to organophosphate pesticides (Hunt et al. 2003, Anderson et al. 2004, ESNERR et al. 2009). High levels of contaminants in harvested crustaceans and bivalves could pose a risk to human health.

4. What are the levels of human activities that may influence water quality and how are they changing?

Human activities that can influence water quality are rated “fair” and a trend is “undetermined.” An important and relatively poorly understood threat to water quality in Elkhorn Slough is non-point source pollution from multiple sources, including substantial agricultural runoff from inputs along the Salinas River, Tembladero Slough, and the Elkhorn Slough watershed. Nutrients and significant concentrations of legacy agricultural pesticides, such as DDT, have been documented in some watershed wetlands, with highest levels in the areas receiving the most freshwater runoff (Phillips et al. 2002, ESNERR et al. 2009). Use of persistent pesticides for agriculture in the area has been phased out, but high concentrations are still present in the sediment and can become re-suspended by erosion (ESNERR et al. 2009). As legacy organochlorines were phased out in the 1970s and 1980s, organophosphate pesticides such as diazinon and chlorpyrifos became widely used, and these pesticides have been found at toxic concentrations in many central coast watersheds (Hunt et al. 2003). Pyrethroid pesticides are now increasingly applied along the central coast and have been found at toxic concentrations in watershed sediments (Anderson et al. 2006, Phillips et al. 2006).

Sediment and freshwater inputs to Elkhorn Slough have been dramatically altered over time through river diversion and modification, such as levee construction. Over 37 miles of levees and embankments were constructed between the 1870s and 1960s in Elkhorn Slough (Van Dyke and Wasson 2005). The diversion of the Salinas River in 1909 and levee construction on the Pajaro River likely led to a significant decrease in freshwater and sediment inputs to Elkhorn Slough. Levees restrict tidal exchange and can reduce water quality due to hypersalinity (ESTWPT 2007, ESNERR et al. 2009).

Over the past ten years management agencies have worked with local stakeholders to create regulatory, monitoring, education, and training programs and to implement better agricultural and urban management practices aimed at reducing or eliminating pollution sources. However, there is a poor understanding of the relationships between the cumulative effects of behavioral changes within the Elkhorn Slough watershed and changes in water quality conditions.

Estuarine Environment Water Quality Status and Trends

#	Issue	Rating	Basis For Judgement	Description of Findings
1.	Stressors		Major alternations to tidal, freshwater, and sediment processes has increased the level of pollution and eutrophication; inputs of pollutants from agricultural and urbanized land sources.	Selected conditions have caused or are likely to cause severe declines in some but not all living resources and habitats.
2.	Eutrophic Condition	-	Low dissolved oxygen levels and high nutrient concentrations are observed but strong tidal flushing dilutes concentrations in main channel.	Selected conditions may inhibit the development of assemblages and may cause measurable but not severe declines in living resources and habitats.
3.	Human Health	?	Elkhorn Slough and connected waterbodies are impaired by pesticides and pathogens. High levels of contaminants in harvested crustaceans and bivalves could pose a risk to human health.	Selected conditions have caused or are likely to cause severe impacts, but cases to date have not suggested a pervasive problem.
4.	Human Activities	?	Substantial inputs of pollutants from non-point sources, especially agriculture. Significant efforts over past ten years to implement best management practices and educate local land owners. No evidence yet of improving water quality due to changes in land management practices.	Selected activities have resulted in measurable resource impacts, but evidence suggests effects are localized, not widespread.

Estuarine Environment Habitat

The following information provides an assessment of the status and trends pertaining to the current state of estuarine habitat.

5. What is the abundance and distribution of major habitat types and how is it changing?

The abundance and distribution of major habitat types in the estuarine environment of the sanctuary is rated “fair/poor” and “declining” due to substantial changes in the relative abundance of estuarine habitat types resulting from over one hundred years of hydrologic alteration. Beginning in the late 1800s, a series of human activities removed marshes from tidal exchange and altered the slough’s basic circulation (Caffrey and Broenkow 2002). These activities included ditching and diking to create pasture for cattle and evaporative salt ponds, and diverting the Salinas River away from Elkhorn Slough, which removed the slough’s major source of freshwater and sediments. The most dramatic change occurred in 1946 when the mouth of Elkhorn Slough was moved to its current location and deepened by more than five times to create a fixed opening to Monterey Bay for Moss Landing Harbor. This alteration to the mouth of the slough is the main cause of subtidal erosion and more recent marsh erosion and conversion. Additional factors that may be contributing to habitat changes in Elkhorn Slough include a decrease in sediment supply due to river diversion, the Monterey Canyon Head that acts as a sediment sink at the mouth of the estuary, sea-level rise, and levee breaching (ESTWP 2007). The observed changes in estuarine habitat abundance and distribution has influenced the associated faunal communities, with declines in some marsh, mudflat, and tidal creek dependent species and increases in the abundance of marine fish and mammals (Van Dyke and Wasson 2005, Ritter et al. 2008).

Analysis of a chronological series of maps and aerial photos by the Elkhorn Slough National Estuarine Research Reserve reveals dramatic changes in the relative abundance of estuarine habitats over the past 130 years (Figure 69). Approximately 65% of Elkhorn Slough habitat was dense salt marsh in 1870, with less than 5% mud and sparse salt marsh habitat. By 2000, the amount of estuarine habitat composed of dense salt marsh had decreased to less than 20% and the amount of mud or sparse salt marsh habitat had increased to approximately 50% (Figure 70, ESNERR, unpubl. data). Marsh drowning and bank erosion, which causes the edges of the marsh to collapse into the channel, is the main cause of this habitat conversion (Van Dyke and Wasson 2005). The tidal prism (the volume of water covering an area between a low tide and the subsequent high tide) has almost tripled since 1956 to 6,400,000 cubic meters (Broenkow and Breaker 2005, Sampey 2006) and tidal erosion results in the export of approximately 56,000 cubic meters of sediment into Monterey Bay each year (Sampey 2006). Field surveys by Elkhorn Slough National Estuarine Research Reserve staff and collaborators show that the banks of the main channel are eroding on average 30 centimeters per year (ESNERR, unpubl. data). The loss of significant sediment inputs to the slough from the Salinas River (diverted in the early 1900s), Pajaro River, and Monterey Bay (due to the jetties) are also considered to be significant in the imbalance of high erosion rates compared with low depositional rates (ESTWP 2007).

Figure 69. Aerial photograph interpretations of changes in estuarine habitat composition in Elkhorn Slough from 1913 to 2000. (Source: Van Dyke and Wasson 2005; Copyright to these images is held by ERF (Coasts and Estuaries))

Figure 70. Analysis of a chronological series of maps and aerial photographs reveals a substantial decrease in dense salt marsh and increase in mudflat and sparse salt marsh over the past 130 years, resulting from human changes to tidal exchange and sediment inputs into the estuary. (Source: ESNERR, unpubl. data)

Erosion of bank and channel habitat is deepening and widening the main channel and tidal creeks and eroding soft sediments from channel and mudflat habitats. The mean cross-sectional area of the main channel increased by approximately 16 percent from 1993 to 2001 (Dean 2003, Malzone 1999). The annual rates of tidal creek widening during the period 1980-2003 were moderate to very high (>0.25 m/yr) across the lower and mid-slough and predominately very high in the upper slough (Van Dyke and Wasson 2005). This widening and deepening of the main channel and tidal creeks has facilitated the colonization of these habitats by large marine fish and mammals. Leopard sharks, bat rays, harbor seals, and sea otters, are now abundant throughout much of the estuary (Harvey and Connors 2002, Yoklavich et al. 2002). The fish fauna in tidal creeks is becoming more similar to that of the main channel (Yoklavich et al. 2002) In addition, the diet of fish in tidal creeks has become more homogenous over time, with a lower diversity of prey items (Lindquist 1998). Continued erosion may lead to the eventual loss of species dependent on tidal creek habitat. In addition, scientists have observed a decrease in fine, unconsolidated sediment along the main channel of Elkhorn Slough since the 1970s (Kvitek et al. 1996). Scour of fine sediment from the subtidal channel between Hummingbird Island and Kirby Park has exposed a harder, more consolidated, older substratum (i.e., hard polished clay and patchy coarse rubble) in portions of the channel creating unsuitable conditions for a number of organisms (Kvitek et al. 1996).

6. What is the condition of biologically-structured habitats and how is it changing?

The condition of biologically structured habitats in Elkhorn Slough are rated “poor” and “declining” based on the severe reduction in abundance of the two native species that form biogenic habitat in the main channel of Elkhorn Slough, eelgrass (Zostera marina) and native oyster (Ostrea lurida, also referred to as Ostreola conchaphila), as compared to historic levels. Though the size of eelgrass beds has been increasing slowly in recent years (ESNERR, unpubl. data), the abundance of native oysters is not improving and may be declining, in part due to competition for attachment sites with a non-native reef-forming tube worm (Ficopomatus enigmaticus) from Australia.

Based on photos and published accounts from the 1930s and early 1940s, eelgrass was very abundant in the central parts of Moss Landing Harbor and the main channel of Elkhorn Slough up to just below Seal Bend (MacGinitie 1935, E. van Dyke, ESNERR, pers. comm.). Recent analysis of historic photographs estimates the area of eelgrass beds to have been approximately 22 hectares (Figure 71; ESNERR, unpubl. data). Beginning in the late 1940s, dredging associated with harbor maintenance and high erosion in the main channel eliminated most of the shallow habitat that eelgrass requires to survive in turbid waters. Eelgrass habitat was reduced to approximately six hectares. In the late 1980s and early 1990s, broadening and shallowing of the main channel in some locations allowed the establishment of an eelgrass bed at Seal Bend and other smaller beds scattered throughout the main channel (Zimmerman and Caffrey 2002, E. van Dyke, ESNERR, pers. comm.). Currently, eelgrass beds are estimated to cover approximately 12 hectares (ESNERR, unpubl. data). The distribution of eelgass habitat is much different than the historical distribution, with the largest bed located at Seal Bend and eelgrass habitat absent from Moss Landing Harbor (Figure 72) Although the current abundance of eelgrass is higher than it was in the middle of the last century, it is still much reduced compared to historic levels (Figure 71). This is a significant conservation concern because eelgrass is a major contributor to productivity in California estuaries and provides important habitat for many invertebrates and fish species (Ricketts et al. 1985, Yoklavich et al. 2002).

Figure 71. Analysis of a chronological series of aerial photographs reveals dramatic loss of eelgrass habitat following the opening of the artificial harbor mouth in 1946. (Source: ESNERR, unpubl. data)

Figure 72. Distribution of eelgrass (Zostera marina), native oyster (Ostrea lurida, also referred to as Ostreola conchaphila), and non-indigenous tubeworm (Ficopomatus enigmaticus), three species that form biogenic habitat in Elkhorn Slough, California. The widest apparent extent of visible submerged eelgrass (green area) was identified from aerial imagery taken in April 2003 (E. van Dyke, ESNERR, unpubl. data) Oysters (blue square) and tubeworms (orange circle) were surveyed along the banks of the main channel in 2003 (Heiman 2006). Small circles/ squares are survey sites where less than 1% of the available surface area was occupied by the focal species, whereas large circles/squares are survey sites where more than 50% of the available substrate was occupied. Click here for a larger image. (Map: S. De Beukelaer, NOAA/MBNMS)

The current population of native oysters is greatly reduced in both size and distribution compared to historic levels. Native oysters were described as very abundant in both the lower and upper slough in the early 1930s (MacGinitie 1935). Currently, extensive native oysters in Elkhorn Slough are limited to a few locations in the upper slough (Figure 72) where they grow on stable, hard substrates, including wood, rocks, and metal (Heiman 2006). There is only one large known intertidal oyster reef, which covers approximately seven square meters and rises 10 to 15 centimeters off of an anthropogenic rock bed (Heiman et al. 2008). More commonly, native oysters in Elkhorn Slough are found in low densities as clumps or as isolated individuals (Heiman 2006, Heiman et al. 2008). The total population size is estimated to be a few thousand individuals (K. Wasson and K. Heiman, ESNERR, pers. comm.). Dead oyster shells are far more numerous than live individuals. Recruitment of new juveniles appears to be very low (K. Heiman, ESNERR, unpubl. data) and there are very few small individuals in the population. Oysters appear to be limited by poor water quality, burial in sediments, and overgrowth by non-native species (Wasson in review).

New biogenic habitat is being created by a non-native reef-forming tubeworm (Ficopomatus enigmaticus) from Australia, which was initially identified in Elkhorn Slough in 1994 (Wasson et al. 2001). Since 1994, F. enigmaticus has spread to a number of sites in the northern half of Elkhorn Slough, with reefs observed in the most northern locations (Figure 72). Because this species requires a small piece of hard substrate to start colony formation, it is in direct competition with the native oysters for hard substrate attachment sites.

7. What are the contaminant concentrations in sanctuary habitats and how are they changing?

The contaminant concentration in estuarine habitats of the Elkhorn Slough watershed is rated “fair” because numerous contaminants from a variety of sources, sometimes appearing in high levels at localized areas, have been identified. In this largely rural watershed, the main source of water and sediment quality degradation appears to be agricultural non-point source pollution (Caffrey et al. 2002). Significant concentrations of legacy agricultural pesticides such as DDT have been documented in some watershed wetlands, with highest levels in the areas receiving the most freshwater runoff (Caffrey et al. 2002). The trend in contaminants in Elkhorn Slough habitats is rated “declining” because of the lack of attenuation of legacy pesticides and the continued input of currently applied pesticides.

A review of the data available from various long-term monitoring programs of environmental contaminants in the Monterey Bay area found that the highest concentrations of many of the contaminants in the database (e.g, chlordane, DDT, dieldrin, PAHs, PCBs) occurred in the Elkhorn Slough and Salinas Valley areas and were probably associated with legacy agricultural applications (Hardin et al. 2007). Moreover, significant relationships between rainfall and lipid-normalized concentrations of dieldrin, DDT, and PCB in mussels from Elkhorn Slough and Moss Landing suggest that suspended sediments in storm runoff is the pathway into the estuary for some contaminants and that the source of these compounds are erodible legacy sources in the surrounding watersheds (Hardin et al. 2007).

Though watershed pollution levels are well documented, there have been few studies of the direct ecological impacts of this pollution on Elkhorn Slough habitats. The reproductive failure of a Caspian Tern colony in 1995 has been attributed to high levels of DDT and other contaminants found in eggs and embryos during a flood year (Parkin 1998). Sediments from the Moss Landing Harbor have been shown to cause toxicity to small crustaceans, and this toxicity has been attributed to organophosphate pesticides (Anderson et al. 2004). In addition to these documented impacts, other ecological changes may be occurring in response to agricultural pollutants, such as losses and declines of species directly due to sensitivity to high contaminant concentrations (ESNERR et al. 2009).

8. What are the levels of human activities that may influence habitat quality and how are they changing?

The greatest threats to estuarine habitats in Elkhorn Slough are the changes to hydrology caused by the estuarine mouth modifications that occurred in 1946, as well as diking and river diversions. These anthropogenic influences are considered to have severely degraded the estuarine portion of the sanctuary, thereby resulting in a “poor” rating. Though many of the structural changes were made many decades ago dredging and maintenance of water diversion structures are on-going human activities that result in the continuing degradation of estuarine habitats (ESNERR et al. 2009).

Agriculture activities in the Elkhorn Slough watershed are the main source of non-point source pollution to estuarine habitats. Significant concentrations of legacy agricultural pesticides such as DDT have been documented in some watershed wetlands, with highest levels in the areas receiving the most freshwater runoff (Caffrey et al. 2002). Management efforts by a number of organizations are aimed at reducing inputs of pollutants to estuarine habitats, however, these management activities have yet to show measurable decreases in contaminants in Elkhorn Slough (ESNERR et al. 2009).

Estuarine Environment Habitat Status and Trends

#	Issue	Rating	Basis For Judgement	Description of Findings
5.	Abundance/Distribution		Over 150 years of hydrologic alteration has resulted in substantial erosion and habitat conversion.	Selected habitat loss or alteration has caused or is likely to cause severe declines in some but not all living resources or water quality.
6.	Biologically-Structured		Severe reductions in the abundance of native structure-forming organisms from historic levels.	Selected habitat loss or alteration has caused or is likely to cause severe declines in most if not all living resources or water quality.
7.	Contaminants		Numerous contaminants present and at high levels at localized areas with limited evidence of community level impacts; on-going input of currently applied pesticides and lack of attenuation of legacy pesticides.	Selected contaminants may inhibit the development of assemblages and may cause measurable but not severe declines in living resources or water quality.
8.	Human Impacts	-	Past hydrologic changes, continued dredging and maintenance of water diversion structures, and input of agricultural non-point source pollution. Management activities have the potential to reduce the input of pollution.	Selected activities warrant widespread concern and action, as large-scale, persistent and/or repeated severe impacts have occurred or are likely to occur.

Estuarine Environment Living Resources

The following information provides an assessment of the status and trends pertaining to the current state of the sanctuary’s living resources in the estuarine environment.

9. What is the status of biodiversity and how is it changing?

Elkhorn Slough contains several estuarine habitats that support a diverse species assemblage. Caffrey et al. (2002) documented dozens of algae and plant species, over 100 fish species, over 300 bird species, and over 550 invertebrate species. Though species richness in the estuary is high, the status of native biodiversity in Elkhorn Slough is rated “fair” based on changes in the relative abundance of some species associated with specific estuarine habitats. Human actions (e.g., altered tidal flow by dikes and channels) have altered the tidal, freshwater, and sediment inputs, which has led to substantial changes in the extent and distribution of estuarine habitat types. There is strong evidence that these changes to estuarine habitats had substantially altered local biodiversity in the past 150 years (Caffrey et al. 2002). However, an overall trend in native biodiversity could not be determined.

Some species that were noted as abundant in portions of the Elkhorn Slough in the 1920 and 1930s are now rarely encountered. Scyphistomae (jellyfish polpys), burrowing sand anemones, the Atlantic soft-shell clam were once common, but were not observed during surveys in the 1970s or in subsequent surveys (Wasson et al. 2002). The native horn snail was likely displaced by the ecologically similar non-native Japanese mud snail (Byers 1999). A number of once common species, including three bivalve species and the blue mud shrimp, may be at drastically reduced levels due to overharvesting for human consumption or use as bait (Wasson et al. 2002).

A comparison of benthic intertidal sediment cores collected in the mid-1970s and mid-1990s found a significant decline in total invertebrate biodiversity over that time period (Wasson et al. 2002). Species that have declined in abundance between the 1970s and 1990s include the phoronid worm (Phoronopsis harmeri), the ghost shrimp (Neotrypaea californiensis), the gaper clam (Tresus nuttallii), and the cephalochordate (lancelet, Branchiostoma californiense). A number of species have increased in abundance, including the fat innkeeper worm (Urechis caupo) and a number of non-native species (e.g., the spionid Streblospio benedicti and the amphipod Grandidierella japonica). Diets of benthic foraging fishes (e.g., sanddab, starry flounder, shiner surfperch) in Elkhorn Slough, which reflect prey availability in core sediment samples, has changed since the 1970s to include increased relative abundance of epifaunal crustaceans and a decrease in infaunal worms (Lindquist 1998).

Habitat heterogeneity in Elkhorn Slough is increasing because of continued changes in the estuary, many of which are due to an increasing tidal prism and on-going changes to water control structures (e.g., berms, dikes, tidegates, culverts). These changes contributed to the subsequent conversion of a few dominant habitat types into a patchwork of several habitat types (Ritter et al. 2008). The loss of fine sediment from various subtidal channels caused a shift from gaper clams to boring clams in portions of the main channel between the 1970s and 1990s (Oliver et al., unpubl. data, as cited in ESNERR 2007). In addition, changes in the relative abundance of large predators may contribute to observed changes in the invertebrate assemblage. A shift in the diet of leopard sharks from clams and crabs in the 1970s to fish and fat innkeeper worms in the 1990s may be due to the increased abundance of southern sea otters in Elkhorn Slough, an important predator of clams, crabs and other large benthic invertebrates (Wasson et al. 2002).

Although eelgrass may be increasing in some areas within the main channel, past losses of eelgrass beds have reduced available nursery habitat for some fishes and invertebrates. For example, two species of polychaete worms and one species of sipunculid associated with eelgrass beds were reported as abundant in the 1930s, but are now rarely encountered (Wasson et al. 2002). Lower abundances of many fish species (for some species 30 percent lower than 1970s abundances) in deep channel sites and an overall decline in diversity from the 1970s to 1990s have occurred in the main channel of Elkhorn Slough and have been attributed to changes in sediment size (Yoklavich et al. 1991, Oxman 1995). In addition, the fish assemblages in the lower channel and tidal creeks have become more similar since the 1970s. Fish assemblages in the tidal creeks now resemble those of the lower slough; this change coincides with the continued erosion and scouring, which has made the geomorphology of the tidal creeks more similar to that of the main channel (Yoklavich et al. 2002).

10. What is the status of environmentally sustainable fishing and how is it changing?

Harvesting of fishes and invertebrates from Elkhorn Slough habitats has occurred for thousands of years (Caffrey et al. 2002). Harvesting by humans for consumption or use as bait is believed to be a factor in the decline of some invertebrates. For these reasons, the question is rated “good/fair.” Changes in harvesting practices and the recent implementation of marine protected areas are the basis for an “improving” trend in the status of environmentally sustainable fishing in Elkhorn Slough.

Digging for clams, shrimp, and worms has occurred during very low tides in the mudflats bordering the lower main channel (Wasson et al. 2002). The limits of take are set by the California Department of Fish and Game and require a sport fishing license. Overharvesting may have been partially responsible for reduced abundance of three species of native bivalve, ghost shrimp, blue mud shrimp, and fat innkeeper worms observed in the 1990s (Wasson et al. 2002). However, very little is known about the effect of human harvesting on invertebrate communities near the mouth of the slough and the effect of this activity may be negligible compared to other influences such as sea otter foraging (Wasson et al. 2002).

Recreational fishing has long been a popular activity in the slough. Organized fishing events like elasmobranch (e.g., sharks, rays) derbies began in the 1940s and continued until 1996. Analysis of catch records from the derbies found some changes in the elasmobranch assemblages, but it is not possible to directly attribute this to the derbies since other factors (e.g. regime shifts, habitat alteration) also influenced the abundance and distribution of elasmobranchs (Carlisle et al. 2007). Recreational hook-and-line fishing has been occurring for decades and mainly targets perches, surfperches, and flatfishes (Yoklavich et al. 2002). There is little historical information on the level of effort or impact on the fish population, but the recent level of take by humans is not thought to have a significant impact on fish populations (Yoklavich et al. 2002).

Two marine protected areas were implemented in 2007 under the Marine Life Protection Act – the Elkhorn Slough State Marine Conservation Area and the Elkhorn Slough State Marine Reserve (see Figure 5). These two contiguous protected areas encompass a large portion of the main channel and marsh habitats of the Elkhorn Slough National Research Reserve. Take of all living marine resources is prohibited, except in the Marine Conservation Area, where finfish may be taken by recreational hook-and-line and clams may be taken on the north shore.

11. What is the status of non-indigenous species and how is it changing?

There is a very high percentage of non-native species in Elkhorn Slough and this question is rated “poor.” A trend of “not changing” was based on no known recent introductions of non-indigenous species. There are significantly higher numbers of introduced species in Elkhorn Slough compared to the open coast. Wasson et al. (2005) documented 527 invertebrate species inhabiting Elkhorn Slough. Of these, 58 were introduced, 25 cryptogenic (i.e., possibly introduced or possibly native), and 444 were native species. In contrast, surveys of adjacent rocky intertidal areas on the open coast documented 588 species, but only eight were introduced, 13 were cryptogenic, and 567 were native species (Wasson et al. 2005). Non-native fish species collected from Elkhorn Slough and surrounding areas include American shad, yellowfin goby, striped bass, and western mosquito fish (Yoklavich et al. 2002).

Some of the most commonly encountered invertebrates during low tide in Elkhorn Slough are non-indigenous species. The Japanese mud snail (Batillaria attramentaria) is the numerically dominant invertebrate on the surface of mudflats in Elkhorn Slough, while the native horn snail (Cerithidea californica), an ecological equivalent, is locally extinct (Byers 1999, 2000). The bright orange sponge (Hymeniacidon sinapium) forms massive aggregations in the upper slough channels with high flow and likely affects the plankton community and its availability as a food source to other filter feeding species (Wasson et al. 2002). Field surveys by researchers with the Elkhorn Slough National Estuarine Research Reserve have been monitoring the relative abundance of the European green crab (Carcinus maenas), first observed in Elkhorn Slough in 1994, and two native crab species. In the early stages of the invasion, the European green crab rapidly increased in abundance as native crabs decreased; in recent years, the European green crabs have declined while the natives have recovered (Figure 73).

The non-native, reef-forming tubeworm (Ficopomatus enigmaticus), which was initially identified in Elkhorn Slough in 1994 (Wasson et al. 2001), has spread to a number of sites in the northern half of Elkhorn Slough, with reefs observed in the most northern locations (see Figure 72 in Question 6). These tubeworms can form calcium carbonate reefs up to one meter high and over five meters in diameter (Heiman et al. 2008). Although they require a small piece of hard substrate to start colony formation, adult tubes can act as hard substrate for subsequent generations, making the potential spread and impact of this species within a system dramatic. At one site, this tubeworm has colonized nearly 100% of the available hard structures, forming reefs that grow out from dock pilings and spread over the surrounding mudflats. The reefs greatly increase the amount of complex hard structure in the slough and create a new, unique habitat that has been shown to enhance the local abundance of invasive species, particularly non-native amphipods and polychete worms (Heiman 2006, Heiman et al. 2008).

Some of the non-indigenous species in the slough were introduced directly from distant locations with non-native oysters during the many decades of oyster aquaculture in the slough. This activity peaked in the 1930s and 1940s and ended in the 1970s (Wasson et. al 2002). The other key mechanism for introduction is hitchhiking on boats from San Francisco Bay or other regional ports with thriving populations of non-native species (Wasson et al. 2001). Oyster culture is not currently occurring in the slough, but the potential for future introductions from fouled boat hulls is high.

Figure 73. Field surveys have documented the invasion of the European green crab in Elkhorn Slough, which rapidly increased in abundance as native crabs decreased. In recent years, the green crabs have declined while the natives have recovered. (Source: ESNERR, unpubl. data)

12. What is the status of key species and how is it changing?

The status of key species, such as native oysters, eelgrass, and salt marsh plants, in the estuarine environment is rated “fair/poor” and the trend is “declining.” Native oysters and eelgrass beds, the main native biologically-structured habitats in the channel, are in poor condition compared to historical levels (see Question 6 in Habitat section relating to the condition of biologically-structured habitats for more information on the status of oysters and eelgrass). Continuing tidal erosion may lead to further declines in these species. Restoration experiments for eelgrass in the late 1980s and early 1990s showed that the general environmental quality in Elkhorn Slough is adequate to support survival and expansion of eelgrass populations if substrate of appropriate depth (0 to 2 m Mean Lower Low Water) and water flow (10-30 cm/s peak flow) is available (Zimmerman and Caffrey 2002).

Pickleweed-dominated salt marsh is critical habitat for a number of marsh-dependant species. Salt marsh provides a number of other ecological functions, including sediment trapping and nutrient retention (Zimmerman and Caffrey 2002). For many decades, erosion and subsidence have converted previously extensive tracts of salt marsh into tidal mudflats (see Figures 69 and 70 in Habitat Section, Question 5). Loss of salt marsh may facilitate further erosion and habitat conversion (Caffrey 2002).

Other species that play an increasingly important role in structuring ecological communities in Elkhorn Slough are not native to the system. It is likely that a number of these non-native species have significant direct and indirect negative impacts on the native faunal assemblage of the slough. For example, the Japanese mud snail out-competes the native horn snail and has completely replaced this native species on mudflats in the upper slough (Byers 1999). European green crabs and the tortellini slugs are voracious predators that affect a number of native invertebrate prey species including native crabs and small bivalves (Wasson et al. 2002).

13. What is the condition or health of key species and how is it changing?

The key species in Elkhorn Slough are eelgrass, native oysters, and salt marsh plants (K. Wasson, ESNERR, pers. comm.). To date, there has been no monitoring of the health or condition of these species. Therefore, this question is rated “undetermined” for both its status and trend. It is suspected that water quality and hydrological issues are negatively affecting these species. Water quality in Elkhorn Slough has been monitored for the last 15 years by the Elkhorn Slough National Estuarine Research Reserve. A recent analysis of the turbidity data found that turbidity had increased at every monitoring site, which has negative implications for the condition of eelgrass habitat (M. Los Huertos, CSUMB, pers. comm.). Contaminants are high in Elkhorn Slough due to inputs from watershed land use practices (Hardin et al. 2007). Estuaries have long served as ecosystem filters, but the present level of anthropogenic input to Elkhorn Slough overwhelms its capacity to clean the water.

14. What are the levels of human activities that may influence living resource quality and how are they changing?

A wide variety of human activities occur in and around the Elkhorn Slough, but there are little data available to quantify the level of these activities and how they have changed over time. Because many human activities exert negative pressures on living resources in the slough, the level of human activities is rated “fair/poor.” Anecdotal information indicates that some of these activities appear to be increasing in intensity while others are decreasing, some in response to recent management actions. However, it is not clear how to combine this information to identify an overall trend, thus the trend in human activities was undetermined.

In 1946, a fixed opening between the slough’s main channel and Monterey Bay was created and contributed to hydrological changes that altered and continue to alter the physical environment and biological communities of Elkhorn Slough. Sediment transportation from watersheds into the slough has also been severely altered by urban development and agricultural activities surrounding the slough. Much of the land surrounding Elkhorn Slough is still used for agriculture, and agricultural runoff leads to nutrient loading, elevated levels of chemical contaminants, and can cause sporadic reproductive failure (e.g., Caspian Tern) or die-offs (e.g., ghost shrimp) (Caffrey et al. 2002).

Past aquaculture practices (e.g., the deliberate introduction of non-native oysters) served as a pathway to introduce non-indigenous species, some of which continue to exert a negative influence on native species. Boating activities within Elkhorn Slough and the adjacent Moss Landing Harbor have facilitated the introduction of non-indigenous species and the potential for future introductions from this activity is high. Boating and kayaking activities related to ecotourism in the slough has increased over the last few decades. These activities have the potential to disturb wildlife, such as mammals and birds, if wildlife-viewing restrictions are not followed.

Harvest of living resources in the slough has been occurring for centuries. Digging for clams, shrimp, and worms in mudflats and fishing with hook-and-line are the two most common activities. Levels of this activity are not well understood, but the recent implementation of the State Marine Reserve and State Conservation Area (see Figure 5) is likely to reduce the amount of living resources harvested from the slough. Duck hunting occurs in the adjacent wildlife area and it is likely that this activity has remained relatively stable.

The Moss Landing harbor houses the intake pipes for the seawater cooling system used by the Moss Landing Power Plant. Entrainment studies indicate that 60% of larvae are lost, but it is not known how this impacts the adult population of fishes and invertebrates in the slough and the adjacent shore (K. Wasson, ESNERR, pers. comm.).

Nearshore Environtment Living Resources Status and Trends

#	Issue	Rating	Basis For Judgement	Description of Findings
9.	Biodiversity	?	Changes in the relative abundance of some species associated with specific estuarine habitats. Overall trend cannot be determined.	Selected biodiversity loss may inhibit full community development and function and may cause measurable but not severe degradation of ecosystem integrity.
10.	Environmentally Sustainable Fishing		There is limited take of shellfish and mudflat invertebrates in the lower slough as well as limited fishing and hunting. New state marine protected areas reduce or eliminate fishing.	Extraction takes place, precluding full community development and function, but it is unlikely to cause substantial or persistent degradation of ecosystem integrity.
11.	Non-indigenous Species	-	High percentage of non-native species, no known recent introductions.	Non-indigenous species have caused or are likely to cause severe declines in ecosystem integrity.
12.	Key Species Status		Abundance of native oyster, eelgrass, and salt marsh are substantially reduced compared to historic levels; continued loss and conversion of salt marsh.	The reduced abundance of selected keystone species has caused or is likely to cause severe declines in some but not all ecosystem components, and reduce ecosystem integrity; or selected key species are at substantially reduced levels, and prospects for recovery are uncertain.
13.	Key Species Condition	?	No direct measurements of health or condition have been made for eelgrass and oysters, and salt marsh.	Not enough information to make a determination.
14.	Human Activities	?	Impacts result from hydrologic modifications, inputs of pollutants from agriculture and development, introduction of non-indigenous species, harvesting, entrainment of larvae in power plant intakes; no clear overall trend in human activities.	Selected activities have caused or are likely to cause severe impacts, and cases to date suggest a pervasive problem.

Estuarine Environment Maritime Archaeological Resources

The following information provides an assessment of the status and trends pertaining to the current state of the maritime archaeological resources in the estuarine environment.

15. What is the integrity of known maritime archaeological resources and how is it changing?

Figure 74. A view of Watsonville Landing (now remembered as Hudson's Landing) after the rail bridge was built across the north end of Elkhorn Slough. (Photo: Elkhorn Slough National Estuarine Research Reserve collection).

The integrity of known maritime archaeological resources in the estuarine environment is “undetermined” because little is known about the integrity of maritime archeological resources in Elkhorn Slough. The Elkhorn Slough area contains Native American midden sites (a feature containing waste products relating to day-to-day human life, such as shellfish, broken animal bones, pottery, arrowheads, etc.), as well as an historic pier known as Hudson’s Landing (also known as Watsonville Landing) (Figure 74). Although there are no known midden sites in the main channel of the slough, there are many midden sites along the edges of the slough. These areas were typically elevated (10-40 feet, or 3-12 meters) and away from a water source in order to avoid aquatic pests (e.g., mosquitoes). In particular, Native Americans occupied an elevated site along the channel 3,000 years before present (and 6,500-8,000 years before present) near the mouth of Elkhorn Slough at the south end of the Highway One Bridge (CA-MNT-229). Mitigation during the upgrade of the bridge in 1985 removed most of the midden.

16. Do known maritime archaeological resources pose an environmental hazard and is this threat changing?

There are no known maritime archeological resources in Elkhorn Slough that pose an environmental threat; therefore this question is rated “good” and “not changing”.

17. What are the levels of human activities that may influence maritime archaeological resource quality and how are they changing?

Existing human activities do not pose a threat to the quality of maritime archaeological resources in Elkhorn Slough. However, as the Elkhorn Slough channel widens and deepens because of erosion, the risk of impact to the Native American midden sites increases. However, management actions under consideration by the Elkhorn Slough Tidal Wetland Project have the potential to decrease the rate of erosion to the channels and tidal creeks, thereby diminishing the threats to the midden sites in the future. Therefore, this question is rated “good.” Currently, the trend of impact to the maritime archeological sites is “not changing.”

Estuarine Environment Maritime Archaeological Resources
Status and Trends

#	Issue	Rating	Basis For Judgement	Description of Findings
15.	Integrity	?	Very little is known for this area.	Not enough information to make a determination.
16.	Threat to Environment	-	No known environmental hazards.	Known maritime archaeological resources pose few or no environmental threats.
17.	Human Activities	?	Existing human activities do not influence archaeological resources.	Few or no activities occur that are likely to negatively affect maritime archaeological resource integrity.

Offshore Environment | Nearshore Environment | Estuarine Environment

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