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State of Sanctuary Resources:
Estuarine and Lagoon Zone

Coastal and Offshore Zone | Estuarine and Lagoon Zone

Water Quality

The following information summarizes an assessment, made by sanctuary staff and experts in the field, of the status and trends pertaining to the current state of water quality in the estuarine and lagoon habitats in the Gulf of the Farallones sanctuary.

1. Are specific or multiple stressors, including changing oceanographic and atmospheric conditions, affecting water quality?

Stressors on water quality, including sedimentation in the estuarine and lagoon areas of the sanctuary, may inhibit the development of the full diversity of species assemblages and may cause measurable but not severe declines in living resources and habitats. For this reason, this question is rated as "fair." There is a trend to reduced erosion and nutrient fluxes in the watershed, but there is a lag before reduced fluxes of nutrients and organic material reach the estuaries and ocean. There is also a lag in changes in estuary morphology following reduction in sedimentation. Overall, it is "undetermined" if there is a detectable trend or change in the number of stressors, although there are signs of hope. Land use pressures have impacted water quality in some of the estuaries in the sanctuary, resulting in changes to sediment and freshwater regimes.

In the case of Estero Americano and Estero de San Antonio, prior sedimentation from erosion in the watersheds has increased the duration of mouth closures in the esteros. Further, the reduced tidal prism (the volume of water covering an area between a low tide and the subsequent high tide) results in reduced flushing and reduced scour of the mouth when it does open. As a result, the esteros may be hypersaline at times (Hickey 2007) or evolve into low-salinity "lakes" if they remain closed for more than a year (J. Largier, Bodega Marine Lab and The Ocean Conservancy, pers.comm.). Similar problems occur in the watershed of Bolinas Lagoon, where diversion of freshwater inputs from creeks and streams flowing into the lagoon and increased sedimentation from natural and anthropogenic sources have reduced the tidal prism of the lagoon (Leet et al. 2001, SWRCB 2006, GFNMS 2008a). The delta near the mouth of Pine Gulch Creek has broadened over the past 20 years, resulting in a loss of tidal prism and accelerated rate of siltation and fill of the lagoon (GFNMS 2008a). Increased sedimentation has also led to the loss of eelgrass beds in Bolinas Lagoon. Measures to help protect and enhance the eelgrass beds in Tomales Bay include establishing no-anchor zones and developing a vessel management plan that addresses illegal and un-permitted moorings. Eelgrass beds have a positive impact on water quality conditions because they sequester nutrients, stabilize sediment and trap pollutants.

Watershed stressors from mining, municipal dumps, leaking septic tanks, livestock grazing, agricultural runoff (primarily animal waste from dairies and rangelands) and vessels can result in high coliform and bacterial contamination, increased sedimentation and contamination with toxic materials (e.g., high mercury levels) in the estuary waters, impairing their health. The state has listed Tomales Bay, Estero Americano and Estero de San Antonio as impaired bodies of water under the 303(d) listing (SWRCB 2006) - see Table 6. The impairments constitute a broad range of impacts, from high nutrient loading to increased siltation and bacteria. Identified water quality impacts result in seasonal closure and rainfall closure of shellfish beds to minimize inputs due to runoff (Table 7).

Table 6
Impaired bodies of water in the sanctuary estuarine habitat as listed under the State 303(d) list. 303(d) lists are prepared as part of the Water Quality Assessment of the state's major water bodies, and meet a requirement of section 303(d) of the federal Clean Water Act. (Source: SWRCB 2006)

Water Segment Source of Impairment Weight of Evidence
Bodega Harbor (adjacent to the sanctuary) Exotic SpeciesSource unknown.
Estero Americano and Estero de San Antonio Nutrients, Sedimentation/Siltation, Total and Fecal Coliform Bacteria, and Indicator BacteriaPasture and range grazing (riparian and upland); intensive animal feeding operations; manure lagoons and dairies in watershed; hydromodification and streambank modification or destabilization; removal of riparian vegetation; nonpoint source for some coliform bacteria.
Tomales Bay: Lawson's Landing, Lagunitas Creek, and Walker Creek and Delta Mercury, Nutrients, Sedimentation/Siltation, and Indicator BacteriaPast surface mining and mine tailings in watershed (leftover substrate); agriculture; upstream impoundment; urban runoff and storm sewers; unknown sources.

Table 7
The number of rainfall closure days, by zone, in Tomales Bay, 2003-2008. See Figure 40 for corresponding map of Growing Area locations, A-D and rainfall closure sections. (Source: CA Dept. of Public Health)

Rainfall closure rules for all conditionally approved commercial shellfish growing areas in Tomales Bay are based on a joint study by the California Department of Health Services and the U.S. Food and Drug Administration conducted in winter 1980. This study concluded that rainfall-related runoff was the principal cause of observed elevated bacterial levels (Source: State of Tomales Bay Proceedings 1992).

table7

2. What is the eutrophic condition of sanctuary waters and how is it changing?

There are high levels of nutrients in the sanctuary's estuaries, but there have been no known mortality events in fish or invertebrates due to eutrophication. There are anecdotal reports of macroalgae eutrophication in sanctuary estuaries, but no regular surveys to properly assess this. The dinoflagellate Alexandrium spp. is a normal constituent of the phytoplankton community along the nearshore and estuarine areas of the sanctuary and is more commonly found than other biotoxin producing phytoplankton, but there have been no reports of high toxin levels in shellfish within the sanctuary since the early 1990s (G. Langlois, CA Dept. of Public Health, pers. comm. 2010). Therefore, selected conditions may preclude full development of living resource assemblages and habitats, but are not likely to cause substantial or persistent declines and this question is rated "good/fair." However, it is "undetermined" if there is a detectable trend or change in the occurrence of eutrophic conditions.

High levels of nutrient input from dairy farm runoff resulted in the designation of impaired water quality on the 303(d) listings (see Table 6, Question 1), but there is a trend to lower inputs. Although summer phytoplankton blooms reduce dissolved oxygen, a 1997 study in Tomales Bay showed acceptable dissolved oxygen levels ranging from 6.0 to 9.5 milligrams per liter (Fourqurean et al. 1997). Additionally, there have not been reported losses of fish populations resulting from these inputs. In addition, the implementation of best management practices has resulted in the reduction of runoff into Tomales Bay from local dairy ranches - and similar practices are being implemented for Estero Americano. Additional studies are required in order to determine to what degree the implementation of the best management practices have been successful and whether estuary conditions have improved.

3. Do Sanctuary waters pose risks to human health?

Figure 40. There are four different rainfall closure zones in Tomales Bay (map showing zones A, B, C and D). (Source: CDPH)
Figure 40. There are four different rainfall closure zones in Tomales Bay (map showing zones A, B, C and D). Click here for a larger image. (Source: CDPH)
There have been consistent closures of aquaculture and shellfish harvesting in Tomales Bay, and to a lesser extent Drakes Estero (within the Point Reyes National Seashore), due to predictable impacts from nonpoint sources of contamination linked with rainfall (see Table 6, Question 1 and Figure 40). Significant rainfall results in levels of indicator bacteria (e.g., fecal coliform) that exceed national standards for commercial shellfish growing areas. The California Department of Public Health has closed shellfish harvesting in Tomales Bay approximately 80 to 110 days per year for the past 10 years as a result of these impacts. There have been two outbreaks of Norovirus in Tomales Bay within the past 10 years, causing gastrointestinal illness in over 170 people (Langlois et al. 1998). For these reasons, this response to this question is rated "fair/poor" because selected conditions have caused or are likely to cause severe impacts, but cases to date have not suggested a pervasive problem. Water quality monitoring in the commercial shellfish growing areas by the state health department since the mid-1980s indicates that there is no discernible improvement or degradation with respect to fecal coliform levels, and therefore, the trend is rated as "undetermined."

Only within the past seven years has water quality monitoring been conducted within swimming areas in the sanctuary. Currently there are several water bodies in the sanctuary region that have been identified as impaired bodies of water on the 303(d) listing (see Table 7, Question 2) as a result of water quality monitoring (SWRCB 2006). The initial data appear to show a slight improvement of water quality for swimming, but more data are needed to determine a trend.

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

Human activities influencing water quality in the estuarine and lagoon areas of the sanctuary have caused or are likely to cause severe impacts, and cases to date suggest a pervasive problem. Therefore this question is rated "fair/poor"; however, conditions are "improving." Federal and state restoration activities have targeted the removal of landfills and have restored, or are in the process of restoring, large portions of mudflats and diked marshes in Bolinas Lagoon and Tomales Bay. Water quality improvements of the Bolinas Lagoon restoration project are expected to include restoration of natural sediment transport and ecological functions of the lagoon, and identification and management of introduced species (GFNMS 2008a). Water quality improvements of the Tomales Bay restoration project are expected to include ongoing monitoring of the bay and tributary streams for pollutants of concern, and monitoring of land use practices and other human influences (Tomales Bay Watershed Council 2007). The education of local agriculture interests by local agencies and institutions has resulted in the implementation of best management practices, which have reduced impacts from nutrient loads and sedimentation, although problems still exist in some areas along both of the esteros and Tomales Bay (GFNMS 2008a). However, it remains to be seen if there is a resulting improvement in water quality in the sanctuary's estuaries.

There continue to be freshwater diversions, resulting in enhanced hypersaline conditions, slower circulation and persistent sand bars across the mouths of the esteros. Freshwater diversions, increased sedimentation and loss of the tidal prism in Bolinas Lagoon have led to the burial and loss of eelgrass beds in the lagoon. Urbanization and increased development within the watershed areas continue to be of concern. It is expected that increased regulation of discharge from vessels, ballast water and aging septic systems will reduce some impacts. Closures of shellfish beds due to polluted runoff will also reduce impacts on humans (but not the impacts on ecological health).

Estuarine and Lagoon Environment Water Quality Status & Trends
table
# Issue Rating Basis For Judgment Description of Findings
1. Stressors
?
Land use pressures have caused changes to sediment and freshwater regimes; increased restoration activities and best management practices may offset water quality problems that have historically resulted in loss of eelgrass beds. Selected conditions may inhibit the development of assemblages, and may cause measurable but not severe declines in living resources and habitats.
2. Eutrophic Condition
?
High levels of nutrient input have caused eutrophication, severe oxygen depletion, and shellfish contamination in the Tomales Bay watershed. However, there have not been associated problems or reported loss of fish populations. Selected conditions may preclude full development of living resource assemblages and habitats, but are not likely to cause substantial or persistent declines.
3. Human Health
?
Nonpoint source contamination has resulted in aquaculture and shellfish closures in Tomales Bay; two Norovirus outbreaks in Tomales Bay. Best management practices have been implemented and further studies are required to determine their success. Selected conditions have caused or are likely to cause severe impacts, but cases to date have not suggested a pervasive problem.
4. Human Activities
Land use pressures have caused changes to sediment and freshwater regimes; loss of eelgrass beds; increased restoration activities, increased regulations, and best management practices may allow for improvements. Selected activities have caused or are likely to cause severe impacts, and cases to date suggest a pervasive problem.

Habitat

The following information summarizes an assessment, made by sanctuary staff and experts in the field, of the status and trends pertaining to the current state of the estuarine and lagoon habitat in the Gulf of the Farallones sanctuary.

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

Figure 41. Aerial view of Bolinas Lagoon. The greatest change to Bolinas Lagoon has been the addition of fill to form the Seadrift community and artifical lagoon seen in the lower portion of the image. (Photo: GFNMS)
Figure 41. Aerial view of Bolinas Lagoon. The greatest change to Bolinas Lagoon has been the addition of fill to form the Seadrift community and artifical lagoon seen in the lower portion of the image. (Photo: GFNMS)
Overall, the status and trend of habitat abundance and distribution in the estuarine environment of the sanctuary is rated "fair/poor" and "not changing" because selected habitat loss or alteration has caused or is likely to cause severe declines in some but not all living resources or water quality. Substantial levels of habitat loss have occurred due to erosion, accretion and habitat conversion. Past human activities, such as diking, mining, dredging, filling and reclamation, have substantially reduced the area of coastal wetlands. Sedimentation has increased in estuaries and bays from activities upstream, such as logging, ranching and agriculture. In Bolinas Lagoon, many historical human activities have caused increased sediment delivery and deposition, which, in turn, have affected some of the physical processes that drive the natural evolution of the lagoon (Leet et al. 2001, Hickey 2007). For example, the results of adding fill for the Seadrift housing development, Highway 1 and Wharf Road directly impact the lagoon, increasing sediment availability and altering the physical processes, thus reducing the tidal prism by as much as 25 percent (Leet et al. 2001). Construction in the floodplains and the rerouting and channelization of creeks has resulted in impaired floodplain functions, in some instances increasing the amount of sediment deposited in the lagoon and reducing the tidal prism (Figure 41). Restoration activities have been planned and some have been implemented, such as the removal or reduction of several invasive species (GFNMS 2008a).

Figure 42. The mean rate of harbor seal flush events (flushes per hour). Flush events can be characterized as disturbances to wildlife resulting from human contact and loss of haul-out spaces. This graph shows that harbor seal flushing event rates in Tomales Bay were reduced after the implementation of a stewardship program in 1996. This program, which was called SEALS, was developed to educate clam diggers on how to avoid accidental flushing of seals while clam digging near their haul-outs (Source: Tezak et al. 2004).
Figure 42. The mean rate of harbor seal flush events (flushes per hour). Flush events can be characterized as disturbances to wildlife resulting from human contact and loss of haul-out spaces. This graph shows that harbor seal flushing event rates in Tomales Bay were reduced after the implementation of a stewardship program in 1996. This program, which was called SEALS, was developed to educate clam diggers on how to avoid accidental flushing of seals while clam digging near their haul-outs. Click here for a larger image. (Source: Tezak et al. 2004).
In general, the abundance of eelgrass beds, eelgrass wracks and marsh vegetation is in decline. Increased sedimentation has lead to the loss of eelgrass beds in Bolinas Lagoon and reduction of some eelgrass beds in the esteros. In addition, the diversion and channelization of streams to control floods and retain water for upland uses has altered the flow of fresh water into Bolinas Lagoon and Tomales Bay. The decreased freshwater input has impacted the conditions in salt marshes, brackish water and eelgrass meadows, causing increased sedimentation and loss of the tidal prism (Airamé et al. 2003, GFNMS 2008a).

There is also the potential for habitat loss at harbor seal haul-out areas. Studies have shown that a combination of disturbance and aquaculture activities have reduced haul-out space available for harbor seals in Tomales Bay and Drakes Estero (in the Point Reyes National Seashore) (Figure 42). Educational programs such as the use of docents and interpretational rangers have reduced disturbance from recreational boaters and clam diggers, which in turn has improved the quality of haul-out areas for harbor seals within these areas (Tezak et al. 2004).

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

The two native species that form biogenic habitat in the estuaries of the sanctuary, eelgrass (Zostera marina) and native oyster (Ostreola conchaphila), have experienced a reduction in abundance from historic levels (Kimbro and Grosholtz 2006). Therefore, selected habitat loss or alteration may inhibit the development of living resources, and may cause measurable but not severe declines in living resources or water quality. For these reasons, this question is rated as "fair" and in "declining" condition.

Figure 43: Sedimentation from culverts draining into Bolinas Lagoon for roadside maintenance can cause burial of seagrass and marsh plants. (Photo: C. Morton, CalTrans)
Figure 43: Sedimentation from culverts draining into Bolinas Lagoon for roadside maintenance can cause burial of seagrass and marsh plants. (Photo: C. Morton, CalTrans)
Studies have shown that Estero Americano and Bolinas Lagoon have suffered substantial loss of eelgrass due to continuing sedimentation causing elevation of substrate and burial of eelgrass beds and root systems (Hickey 2007, Leet et al. 2001). In the case of Bolinas Lagoon, the development that has taken place both upland and around the estuary has severely impacted the system's ability to discharge its sediments into the ocean and scour deeper channels. Bolinas Lagoon has also undergone increased urbanization and fill, sedimentation from roadside and coastal armoring, diversion of freshwater, reduction of the tidal prism and a subsequent decrease in scouring effect (Figure 43) (GFNMS 2008a). Such sedimentation can bury eelgrass and oyster beds, although rates are improving in Tomales Bay due to recent restoration efforts (Kimbro and Grosholtz 2006). Tomales Bay has also shown substantial loss of native oyster beds. Such problems are largely the result of human-caused impacts, such as past coastal armoring, increased moorings, anchoring and abandoned vessels impacting the benthic habitat, and roadside maintenance activities that result in increased sediment discharges, causing a decline or change of the tidal prism.

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

There is limited contaminant monitoring work taking place in the estuaries of the sanctuary. Therefore, the status and trend rating for contaminant concentrations are both "undetermined" until further monitoring can be conducted. Studies on benthic clams in Walker Creek in Tomales Bay have shown high levels of mercury, most likely resulting from impacts of past mining operations. The nearby Gambonini mercury mine was in operation in the 1960s and early 1970s (USEPA 2001, SFBRWQCB 2005). Mine tailings (leftover substrate) were stored on-site, but a major storm event in 1982 resulted in the release of tailings into Walker Creek, the second largest tributary in Tomales Bay. Water quality studies suggest that hundreds to thousands of kilograms of mercury were discharged from the mine site into downstream waters. In 1998, the U.S. Environmental Protection Agency initiated a Superfund cleanup action at the site in order to eliminate (to the maximum extent feasible) the discharge of mercury-laden soil and sediments from the 12-acre mining waste pile, ultimately reducing the impacts from past mining activities (Gassel et al. 2004). The discharge from the mine has been halted and restoration of the mine has been completed, but contaminants in the Walker Creek delta continue to be of concern.

NOAA's Mussel Watch program, a long-term monitoring program of pollutants in the marine environment, has stations in Bodega Bay and Tomales Bay. Contaminants tested include persistent organic pollutants (e.g., butyltin, chlordane, DDT, dieldrin, PAHs and PCBs) and trace metals (e.g., arsenic, cadmium, copper, mercury, nickel, lead tin, and zinc). Monitoring data indicates that there is no upward or downward trend for persistent organic pollutants or trace metals at these two stations. Concentrations for almost all of these contaminants in mussels were either low or medium level (comparable to nationwide results). The one exception was cadmium at the Bodega station, which was relatively high. However, cadmium is naturally occurring in seawater and has been known to be elevated in upwelling areas along the West Coast, so this may reflect a natural occurrence. (Kimbrough et al. 2008).

Limited data show elevated levels of contamination in harbors and marinas of San Francisco Bay and may indicate a need to assess impacts from the small marinas and boat-work operations within Tomales Bay and Bolinas Lagoon. The degree of contamination of these sites relates to the density of vessel traffic, the intensity of boat-works (e.g., scraping and painting), and the extent of flushing of the water bodies concerned. Flushing is often poor in harbors and marinas, permitting a build-up of contaminants (Phillips 1987).

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

The level of human activities influencing the habitats in the estuaries of the sanctuary is rated as "fair" and the trend as "stable" because measurable habitat impacts related to urbanization and poor land use practices continue to occur, but evidence suggests effects are localized, not widespread. Past human activities, such as diking, mining, dredging, filling and reclamation, have substantially reduced the area of coastal wetlands. Sedimentation has occurred in estuaries and bays from activities upstream, such as logging, ranching and agriculture. Road construction and coastal armoring continues to be a problem along sections of the coastal highway (Bolinas and Tomales) and in other areas of coastal development. Although localized, these activities can have a high impact as they can convert the habitat type, increase erosion rates and have the potential to result in large-scale debris.

Poor upland practices have contributed to increased pollutants because of loss of tidal prism and flushing capabilities in the sanctuary estuaries. The discharges from the now-closed Gambonini mercury mine have been halted and restoration of the mine has been completed, but contaminants in the Walker Creek delta within Tomales Bay continue to be of concern.

Vessel activities and recreational shell fishing has caused abandonment of marine mammal haul-outs in Tomales Bay and Bolinas Lagoon. Increased management activities such as outreach programs have reduced disturbance that in turn has improved the quality of haul-out areas for harbor seals within the sanctuary (Tezak et al. 2004).

Vessel propellers, anchors, anchor dragging to keep channels open and moorings can damage the underground root and rhizome system of eelgrass and impact oyster beds. There has been an increase in the number of moorings in Tomales Bay (GFNMS 2006, unpub. data). A new regulation to protect eelgrass prohibits anchoring in seagrass beds in Tomales Bay. Management actions to address mooring have been identified, and a vessel management plan is currently being developed. There is hope that California's Nonpoint Source Pollution Control Program, which designates critical coastal areas and applies special management measures to minimize impacts on water quality, will also help decrease vessel impacts. Poor upland practices such as water diversion and increased sedimentation have also caused loss of eelgrass beds in Bolinas Lagoon.

Fishing activities can also displace eelgrass and oyster beds. Further, mariculture of several bivalve species in Tomales Bay includes potential negative impacts: (i) the presence of mariculture-farming equipment can reduce eelgrass cover and alter sediment deposition patterns; (ii) maintenance operations can trample sediments and damage eelgrass beds; and (iii) bivalve shells and associated farming equipment often provide large amounts of hard substrate habitat that is not naturally present, thus altering species communities (Carr et al. 2008).

Management and restoration efforts may lessen the impacts caused by human activities. Examples include the reduced impact of the mercury mine, implementation of best management practices to reduce runoff, and the restoration activities that are taking place in the sanctuary, in addition to efforts such as developing a vessel management plan to address illegal moorings in eelgrass, and the removal of abandoned vessels from Tomales Bay.

Estuarine and Lagoon Environnent Habitat Status & Trends
table
# Issue Rating Basis For Judgment Description of Findings
5. Abundance/Distribution
Habitat loss due to erosion, habitat conversion, and sedimentation. 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. Structure
Loss of eelgrass in Bolinas Lagoon due to watershed issues causing sedimentation and elevation of mudflats. Loss of native oyster beds in Tomales Bay due to sedimentation, roadside maintenance activities, anchoring and mooring. Selected habitat loss or alteration may inhibit the development of living resources, and may cause measurable but not severe declines in living resources or water quality.
7. Contaminants
?
Limited data, though bird studies in other estuarine areas strongly suggest the need for increased monitoring. N/A
8. Human Impacts
Impacts from continued land use, urbanization, erosion, pollutants from closed mines, and vessel activities may be offset by reduced mining activities, restoration activities and new regulations. Selected activities have resulted in measurable habitat impacts, but evidence suggests effects are localized, not widespread.

Living Resources

The following information summarizes an assessment, made by sanctuary staff and experts in the field, of the status and trends pertaining to the current state of the living resources found in the estuarine and lagoon environment of the Gulf of the Farallones sanctuary.

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

Biodiversity in the estuaries of the Gulf of the Farallones sanctuary is rated "fair/poor" and "declining," because it is probable that selected habitat loss or alteration has caused or is likely to cause severe declines in some but not all ecosystem components and reduce ecosystem integrity. The principal reason for the low rating is the loss of eelgrass (Zostera marina), a key habitat for estuarine species, particularly in Bolinas Lagoon (T. Moore, CDFG, pers. comm.). The main cause of this loss appears to be sedimentation caused by human activities (see Question 6). Eelgrass is important in that it provides refuge, food source and nursery space that supports a rich diversity of fish and wildlife, including many commercially and recreationally important fish species, shorebirds, waterfowl, crabs, shrimp and many other invertebrates. The loss of eelgrass beds has a cascading affect on the countless other species that depend on this habitat for survival. Ten to 100 times more animals can be found in eelgrass beds compared to adjacent sandy and muddy habitats (Olyarnik 2007). In addition, the establishment of invasive species, such as green crabs and mud snails, is expected to continue to impact these relatively small ecosystems. In general, introduced species in the marine and estuarine environment alter species composition, threaten the abundance and/or diversity of native marine species, interfere with the ecosystem's function and disrupt commercial and recreational activities (GFNMS 2008a).

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

Currently, there is limited commercial fishing in the estuaries of the sanctuary. Extraction does not appear to affect ecosystem integrity (full community development and function) and, therefore, this question is rated "good" and "not changing." Fishing in the estuaries includes commercial harvest of oysters in aquaculture facilities, sport take of clams, and some fishing for herring, rock crab, perch and halibut, all in Tomales Bay. Generally, however, there is not a great deal of commercial or recreational extraction in the estuaries, and targeted species are highly variable depending on environmental conditions (e.g., El Niño influences and sedimentation shifts). Further, there is little information on the changes in these and other estuarine populations that could result from fishing.

The productivity of estuaries and lagoons may change with large-scale fluctuations in climate. Populations of some species, including salmonids, vary with climate fluctuations and changes to migration corridors and spawning habitats. For example, in the mid-1970s, the Pacific changed from a cool water regime where anchovy dominated to a warm water regime where sardine dominated. A shift back to an anchovy regime occurred in the middle to late 1990s (Chavez et al. 2003). These changes in salmonid forage fish may have cascading trophic impacts.

Figure 44. Annual counts of Chinook salmon in the Russian River. The adult run begins in late August, although relatively few fish are observed prior to October. Typically, the run peaks October through mid-November, and continues through the end of December.
(Source: Sonoma County Water Agency)
.
Figure 44. Annual counts of Chinook salmon in the Russian River. The adult run begins in late August, although relatively few fish are observed prior to October. Typically, the run peaks October through mid-November, and continues through the end of December. Click here for a larger image.(Source: Sonoma County Water Agency)
The disturbance and destruction of upland salmon spawning habitat has resulted in declines of all populations of salmon. Several subpopulations of Chinook salmon (Figure 44), Coho salmon, and steelhead trout in Central California are extinct, and the remaining populations have been listed as federally endangered and threatened. A significant percentage of salmon remaining in California waters are raised in hatcheries. Salmon habitat restoration projects are helping to restore a few of these populations.

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

There is a high number of non-indigenous species in the estuarine zones of the sanctuary. Because non-indigenous species have caused or are likely to cause severe declines in some but not all ecosystem components and reduce ecosystem integrity, this question is rated "fair/poor." There is little monitoring data to determine the trend, therefore this question is rated as "undetermined." There are significantly higher numbers of non-indigenous species in the estuaries of the sanctuary in comparison to the offshore zone. It is estimated that about 143 species of invasives are present in the sanctuary, most of which exist in the estuarine zone (Byrnes et al. 2007), the most potentially harmful being European green crabs (Carcinus maenas), Japanese mud snails (Batillaria attramentaria) and smooth cordgrass (Spartina alterniflora) and its hybridization with the native cordgrass, Spartina foliosa.

The extent, geographical coverage and ecosystem impacts of non-indigenous species within the sanctuary are currently unknown. European green crabs are a threat because they can prey on and compete for resources with native crabs, such as rock crabs and Dungeness crabs, and as such may have profound impacts on the commercial fishery (Cohen 1997). Japanese mud snails reach extraordinary densities over significant areas of high intertidal mudflats, suggesting the potential for substantial impacts to sedimentary environments as well as both infaunal and epifaunal communities (Dewar et al. 2008). As recently as 2003, smooth cordgrass has invaded many acres of mudflat habitat in San Francisco Bay, resulting in loss of habitat for salmon and oysters, and economic losses for those who rely on these species (Brusati 2008). On a smaller scale, smooth cordgrass has appeared in Tomales Bay and Bolinas Lagoon, but is under control.

There is also concern about the proliferation of the gem clam (Gemma gemma) in Bolinas Lagoon and Tomales Bay (Byrnes 2007, USFWS 2005). The success of the gem clam has been triggered by the invasion of the European green crab that thrives on native clams in the central and Northern California estuaries. Historically, native clams have kept the gem clam stabilized. With the invasion of the green crab, gem clams are now becoming a potential threat to the ecosystem (Milius 2005). The sanctuary, along with partners from UC Davis and the Smithsonian, are attempting to control green crabs in Bodega Harbor and a manmade lagoon adjacent to Bolinas Lagoon.

12. What is the status of key species and how is it changing?5

In estuaries, the reduced abundance of selected keystone species may inhibit full community development and function, and may cause measurable but not severe degradation of ecosystem integrity. Therefore, key species are considered to be in "fair" condition, but with a "declining" trend. Key species particularly important to these habitats include eelgrass, tidewater goby and Brant. There are many other key species located in the estuarine and lagoon zones of the sanctuary, including herring, leopard shark, bat ray, harbor seal, Snowy Plover and Brandt's Cormorant.

Eelgrass (Zostera marina) is a keystone species that has shown signs of decline in some estuaries, including nearly extinct levels in Bolinas Lagoon (Leet et al. 2001, GFNMS 2008a). However, further analysis is necessary to confirm the decline - including determining the amount of eelgrass that is currently in the sanctuary. The greatest limiting factor for eelgrass populations in the bays and estuaries of the sanctuary is water clarity and water quality. Turbidity from sediment runoff and in-water construction activities inhibits eelgrass from receiving sunlight, which in turn reduces its ability to photosynthesize. An increase in sedimentation also forces the eelgrass to grow closer to the surface, thus exposing the beds to increases in temperature. Also, decreases in water quality promote algal growth, which increases epiphytes (plants that grow on other plants) on eelgrass, weighs down the leaves and shades the plants from receiving sunlight. Other physical disturbance such as scars from boat propellers and anchor chains also degrade the integrity of the beds. The loss of eelgrass has the possibility to instigate the decline of a number of species that depend on it, thus prompting ecosystem-level changes.

Although the endangered tidewater goby (Eucyclogobius newberryi) appears to be stable and locally abundant in some sanctuary estuaries, including Estero Americano and Estero de San Antonio, in general their abundance has declined substantially due to habitat loss and degradation and poor salinity and other water quality conditions (USFWS 2005). Brant (Branta bernicla) population levels are increasing, but recovery is slow because they are affected by climatic changes in their northern breeding areas and by increased frequency and severity of El Niños (Reed et al. 1998, Schuchat 2006). In 1987, these geese were noted in the first sanctuary management plan (GFNMS 1987) as a species of concern and in decline. Today, the Brant population has increased and many are seen foraging on seagrass and algae in Tomales Bay.

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

Insufficient data exist on the health of key species in the estuarine zone of the sanctuary (see Table 5, Question 5 in Offshore section); therefore, the status and trend are considered "undetermined" at this time. Some fish have been found to exhibit high levels of mercury, but this relates more to their suitability for human consumption than to their overall health. Methylmercury can be passed up the food chain to piscivorous (fish-eating) birds and mammals (Weiner et al. 2003, Bond and Diamond 2009). However, it is thought that humans are not at risk from eating fish from Tomales Bay because, in general, most fish are not feeding solely within the bay. The EPA recommends that the state uses a screening level of 0.3 mg/kg when measuring methylmercury levels in fish (SFBRWQCB 2005, USEPA 2001). Of the 14 fish samples tested in the sanctuary in 2001, 12 were over the recommended limit of 0.3 mg/kg (SFBRWQCB 2007). Harbor seals appear to be doing well in both Tomales Bay and Bolinas Lagoon, but disturbance levels may be increasing in Tomales Bay, which could eventually affect their health (Tezak et al. 2005).

Unfortunately, data on condition do not exist for most other estuarine species. Additional testing of higher trophic levels of birds, mammals and fish in Tomales Bay are needed in order to determine trends and impacts on sanctuary estuarine resources in Tomales Bay.

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

In estuaries, human activities influencing living resource quality are primarily past impacts caused by runoff and illegal discharges, wildlife disturbance, and urbanization. Therefore, selected activities have caused or are likely to cause severe impacts, and cases to date suggest a pervasive problem, and the response for this question is rated "fair/poor." Although some detrimental activities are decreasing in intensity, others known to be harmful are increasing; therefore, the overall trend is rated as "declining." A number of management actions are underway to minimize impacts, but their success remains to be determined.

The frequency of oil spills has decreased in recent years, but some activities that cause wildlife disturbance (e.g., boating and excessive visitation) are increasing. Illegal discharges associated with higher visitation are also likely increasing. There has also been an increased loss of biodiversity due to increased sedimentation caused by human activities such as poor upland practices and vessel activities. The disturbance and destruction of upland salmon spawning habitat has resulted in declines of all populations of salmon. Levels of anchoring, runoff from agricultural or developed lands, and trampling of intertidal communities are all probably not changing at present. Levels of recreational clam digging, kayaking and motor boating are variable and these activities sometimes causes disturbance to harbor seals on their haul-outs (Tezak 2005). Unfortunately, for other potentially damaging activities, the trends are unknown. Two of these include poaching and upland hydro-modification caused by agricultural practices and urbanization.

A decline in the productivity of estuaries and lagoons may be associated with long-term variation in climate. Populations of some species, including salmonids, vary with climate fluctuations and changes to migration corridors and spawning habitats.

Introduced species have caused a loss of biodiversity. A species inventory of the introduced and invasive species within the sanctuary's estuarine habitats has been compiled, but there are no formal monitoring programs or formal plans to control or eliminate the most destructive species or new invaders. Presently, there are attempts by Marin County and the University of California to control cordgrass on the mud flats of Tomales Bay, and county management controls have eradicated it in Bolinas Lagoon. Attempts are also currently underway to control green crabs in Seadrift Lagoon and Bodega Harbor, both of which are adjacent to the sanctuary. There is a need for heightened outreach programs to prevent accidental releases of non-native species within the sanctuary's estuaries.

Estuarine and Lagoon Environment Living Resources Status & Trends
table
# Issue Rating Basis For Judgment Description of Findings
9. Biodiversity
Species diversity changes due to eelgrass loss in Bolinas Lagoon and invasive species. Selected biodiversity loss has caused or is likely to cause severe declines in some but not all ecosystem components and reduce ecosystem integrity.
10. Extracted Species
up arrow
Minimal extraction. Extraction does not appear to affect ecosystem integrity (full community development and function).
11. Non-indigenous Species
?
High numbers of invasive species including European green crabs, Japanese mud snails and smooth cordgrass. Limited data are available on the density or geographic extent of most non-indigenous species. Non-indigenous species have caused or are likely to cause severe declines in some but not all ecosystem components and reduce ecosystem integrity.
12. Key Species
down arrow
Keystone and some key species are at reduced levels; eelgrass decline in Bolinas Lagoon is likely to diminish recovery potential; abundance of the tidewater goby has declined substantially due to habitat loss and degradation; brant populations had been on the decline and are now increasing, but recovery is slow. The reduced abundance of selected keystone species may inhibit full community development and function, and may cause measurable but not severe degradation of ecosystem integrity; or selected key species are at reduced levels, but recovery is possible.
13. Health of Key Species
?
Insufficient data. Some fish have high mercury levels; it is unknown how this may impact fish populations. Disturbance to harbor seals may impact their health. N/A
14. Human Activities
Impacts resulting from urbanization, changing uses that affect watersheds, and wildlife disturbance caused by visitor activities; management activities to increase monitoring of and outreach about introduced species are needed; restoration planning needs to be implemented in Bolinas Lagoon and completed for vessel activities in Tomales Bay. Selected activities have caused or are likely to cause severe impacts, and cases to date suggest a pervasive problem.

Maritime Archaeological Resources

The following information summarizes an assessment, made by sanctuary staff and experts in the field, of the status and trends pertaining to the current state of maritime archaeological resources in the estuarine and lagoon zone in the Gulf of the Farallones sanctuary.

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

Figure 45. More than 30 shipwrecks have occurred at Duxbury Reef (located seaward, outside of the sanctuary's estuarine zone), so named for the sailing ship Duxbury that struck the reef in 1849 but later was floated off and saved. Two more victims that became stranded on the reef in close proximity were the four-masted schooner Polaris (1914; background) and steam schooner R. D. Inman (1909; forefront). (Photo: James Shuttleworth Collection)
Figure 45. More than 30 shipwrecks have occurred at Duxbury Reef (located seaward, outside of the sanctuary's estuarine zone), so named for the sailing ship Duxbury that struck the reef in 1849 but later was floated off and saved. Two more victims that became stranded on the reef in close proximity were the four-masted schooner Polaris (1914; background) and steam schooner R. D. Inman (1909; forefront). (Photo: James Shuttleworth Collection)
The only known archaeological resources in the estuarine environment of the sanctuary are contained in Tomales Bay (Figure 45). There are seven wrecks in Tomales Bay, five of which are schooners (Anglo-American, Marin and European6 were lost in 1861, the H. Caroline in 1874, and the Hannah B. Bourn in 1868). The Hayes7, an unknown rig, was lost in 1869. Finally, a salmon trawler was reported lost at a reef near Dillon Beach in 1929. The integrity and trend of these resources is "undetermined," because these sites have not been visited or investigated by federal, state or private resource management agencies.

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

Because the majority of the wrecks in the estuarine environment of the sanctuary are schooners and it is unlikely that they were carrying hazardous cargo, there is very little chance that they pose an environmental hazard. It is possible, however, that the salmon trawler could potentially pose a threat, releasing pollutants if it is disturbed. Therefore, selected maritime archaeological resources may pose isolated or limited environmental threats, but substantial or persistent impacts are not expected, and this question is rated "good/fair" with an "unchanging" trend.

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

Several human activities may influence the quality of maritime archeological resources in the estuarine environment, including bottom fishing (primarily from the herring fishery), aquaculture activities, anchoring and mooring. Although piers are not currently being constructed in the estuaries in the sanctuary, such an activity could disturb and possibly damage submerged archaeological resources. Environmental restoration, such as oyster recovery programs, could also impact the maritime archeological resources by disturbing or burying them. Current restoration plans for habitats and living resources do not consider integration of impacts on the submerged maritime and other cultural resources. Because some potentially relevant activities exist (e.g., restoration of oysters and seagrass beds, establishment of long-term mooring areas, and removal of derelict vessels), but do not appear to have had a negative effect on maritime archaeological resource integrity, this question is rated "good/fair." A trend cannot be determined due to a lack of monitoring data.

Estuarine Environment Maritime Archaeological Resources
Status and Trends

table
# Issue Rating Basis For Judgment Description of Findings
15. Integrity
?
No wreck sites have been visited or investigated. N/A
16. Threat to Environment
Unlikely that the wrecks (mostly schooners) contain hazardous cargo. Selected maritime archaeological resources may pose isolated or limited environmental threats, but substantial or persistent impacts are not expected.
17. Human Activities
?
Bottom fishing, aquaculture and habitat and living resource restoration activities could affect resources. Some potentially relevant activities exist, but they do not appear to have had a negative effect on maritime archaeological resource integrity.

. . . . . . . . . . . . . . . .
5 See Table 5 (Living Resources Question 12 in Coastal /Offshore Zone section) for a complete listing of key species in the sanctuary

6 European was probably a small, two-masted schooner involved in the early coastal trade. She does not appear in any vessel registries around the time of her loss. The Bancroft Library holds a citation from the Congressional Record, in which it is stated that the schooner European was a partial loss at Bodega Bay in October 1861. In Mitchell's The Commerce of the North Pacific Coast, European is mentioned as having been lost while bound for Timber Cove, and as having been worth $5,000. To the contrary, however, another source claims that a vessel named European was wrecked at Tomales Bay in 1861. Delgado, James P. & Haller, Stephen A., 1989, Submerged Cultural Resources Assessment: Golden Gate National Recreational Area, Gulf of The Farallones National Marine Sanctuary and Point Reyes National Seashore, National Park Service, Santa Fe, NM 7 Hayes is the name of a vessel reported wrecked at Tomales Bay in 1869. No vessel of this name appears in the registers around that time, and no further information about the incident has surfaced during this research. Delgado, James P. & Haller, Stephen A., 1989, Submerged Cultural Resources Assessment: Golden Gate National Recreational Area, Gulf of The Farallones National Marine Sanctuary and Point Reyes National Seashore, National Park Service, Santa Fe, NM

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