Greater Farallones National Marine Sanctuary: Summary of Resource Conditions

The various resource status and trend evaluations presented in this report are summarized below. Each question used to rate the condition of and trends in sanctuary resources is listed, followed by:

1. A set of rating symbols that display key information. The first symbol includes a color and term to indicate status, the next symbol indicates trend, and a shaded scale adjacent to both symbols indicates confidence (see key for example and definitions).
2. The status description, which is a statement that best characterizes resource status and corresponds to the assigned color rating and definition as described in Appendix A. The status description statements are customized for all possible ratings for each question.
3. The rationale, which is a short statement or list of criteria used to justify the rating.

Key:

Drivers and Pressures

Question 1: What are the states of influential human drivers and how are they changing?

Rationale: ONMS and GFNMS staff decided not to rate the status and trend of influential human drivers at GFNMS. The primary purposes for rating the status and trends of resources are to use condition reports to assess program effectiveness and to influence management of human activities and certain natural resource actions. For the most part, drivers are not manageable, at least not under the authority of the National Marine Sanctuaries Act, nor do most of them originate at scales relevant to national marine sanctuary management. While understanding them is important, rating them is not necessary to achieve the goals of the condition report.

Question 2: What are the levels of human activities that may adversely influence water quality and how are they changing?

Coastal and Offshore Region

Status Description: Selected activities have caused measurable resource impacts, but effects are localized and not widespread or persistent.

Rationale: Consideration of both land- and sea-based activities that pose threats to water quality indicated a mix of improving and worsening threats. While the number of transits by large commercial shipping vessels remained consistent throughout the study period, the distance transited through the sanctuary decreased. Cruise ships reported illegal discharges in the sanctuary during the study period. However, there was a decrease in the number of discharge incidents and volume discharged from barges transporting dredged materials, as well as a decrease in the number of large oil spills. Lastly, there was a minor increase in land use along the coast in recent years.

Estuarine and Lagoon Region

Status Description: Selected activities have caused measurable resource impacts, but effects are localized and not widespread or persistent.

Rationale: There is a limited amount of quantitative data on human activities that may affect water quality in GFNMS estuarine and lagoon habitats. Although remediation has occurred at the inactive Gambonini Mine, mercury remains elevated in Walker Creek and the Walker Creek Delta. Vessel activities, which elevate the risk for petroleum product releases and potentially human waste discharge, remain popular in Tomales Bay. There was a minor increase in developed high-intensity land use, but the associated impacts to water quality in sanctuary estuaries are unknown. Oil releases from vessels and vehicles occurred, but the volumes and impacts are generally unknown.

Question 3: What are the levels of human activities that may adversely influence habitats and how are they changing?

Coastal and Offshore Region

Status Description: Selected activities have caused measurable resource impacts, but effects are localized and not widespread or persistent.

Rationale: Marine debris was documented on beaches regionally and on the surface and the seafloor in GFNMS. The most commonly found type of debris on the seafloor was commercial fishing gear. Trawling and crab fishing activities occur each year through large areas of the sanctuary. In 2020, more areas were opened to trawling in GFNMS. Easy access to some rocky reefs in the sanctuary, such as Duxbury Reef, resulted in comparatively high human visitation. The lack of baseline data for these indicators prevented the determination of a trend.

Estuarine and Lagoon Region

Status Description: Selected activities have caused measurable resource impacts, but effects are localized and not widespread or persistent.

Rationale: There is limited information on specific human activities that may adversely impact estuarine and lagoon habitat in GFNMS, and ratings were based on a limited number of relevant indicators for which information was available in Tomales Bay. Removal of moorings from eelgrass beds since 2016 reduced the potential for damage to eelgrass habitat. Marine debris was consistently present in Tomales Bay despite some removal efforts. Clamming activities continued to occur, and activity was likely lower compared to historic levels, though data were limited. Little to no data were available for all indicators for Bolinas Lagoon, Estero Americano, and Estero de San Antonio.

Question 4: What are the levels of human activities that may adversely influence living resources and how are they changing?

Coastal and Offshore Region

Status Description: Selected activities have caused measurable living resource impacts, but effects are localized and not widespread or persistent.

Rationale: Vessel activities and trap fisheries affected living resources through ship strikes and entanglement, potentially affecting the recovery of threatened and endangered species. Although these activities do not appear to have substantially changed during the study period, changes in whale distribution increased the risk of ship strikes and entanglements. Pinnipeds and seabirds were also observed entangled in trash and fishing gear during the study period; entanglement trends for these species were variable, and there were no apparent effects on abundance of these species in the sanctuary. Although there were some exceptions, human activities that disturb seabirds and harbor seals generally remained stable or decreased, and did not appear to affect wildlife abundance or use of the sanctuary. There were no substantial oil spills in the sanctuary during the study period, and tar ball deposition was infrequent (and likely resulted from natural seeps).

Estuarine and Lagoon Region

Status Description: Some potentially harmful activities exist, but they have not been shown to degrade living resource quality.

Rationale: Disturbances to wildlife were documented, but these did not appear to hinder use of the sanctuary by wildlife. Human activities in GFNMS estuarine habitats were stable from 2010–2019, but increased in 2020–2021. Oil pollution from vessels and vehicles was observed but not quantified in Bolinas Lagoon and Tomales Bay.

Question 5: What are the levels of human activities that may adversely affect maritime heritage resources and how are they changing?

Coastal and Offshore Region

Status Description: Some potentially damaging activities exist, but they have not been shown to degrade maritime heritage resource condition.

Rationale: The levels of human activities that may adversely affect maritime heritage resources are not thought to have caused widespread impacts during the study period; for some indicators, no adverse impacts are known. Potentially damaging human activities in the coastal and offshore region of the sanctuary have occurred, including scuba diving and commercial fishing, but these are not thought to have caused widespread impacts during the study period. Anecdotal information from divers indicated a decrease in looting at maritime heritage sites since sanctuary designation, and no looting was documented during the study period. Additionally, there was no new nearshore or offshore development in the coastal and offshore region of GFNMS. A few adverse impacts were observed; for example, commercial fishing gear was documented on two shipwrecks, the SS Selja and the TV Puerto Rican. Climate impacts are likely occurring and are of concern, but difficult to measure without comprehensive site baseline data or regular monitoring. The lack of systematic monitoring of all GFNMS maritime heritage sites limited this assessment.

Estuarine and Lagoon Region

Status Description: Few or no activities occur at maritime heritage resource sites that are likely to adversely affect their condition.

Rationale: There is one known historic maritime heritage resource in the estuaries of GFNMS, the shipwreck Oxford. The remains of the wreck are submerged and buried under sediment, which provides a measure of protection from human activities. During the study period, only one research activity allowing contact with the submerged lands at the shipwreck site was permitted, to confirm the wreck’s presence. This research activity likely had negligible adverse impacts on the wreck. The site has not been revisited for further research. Oxford is not located where vessels are known to anchor. Commercial herring fishing was low during the study period compared to historic levels and has not resulted in known adverse impacts on the wreck. There are data gaps for all indicators, particularly related to climate change, and there is a need to determine if there are other maritime heritage resources in the GFNMS estuarine and lagoon region.

Water Quality

Question 6: What is the eutrophic condition of sanctuary waters and how is it changing?

Coastal and Offshore Region

Status Description: Eutrophication has not been documented, or does not appear to have the potential to negatively affect ecological integrity.

Rationale: Eutrophication was not detected in the coastal and offshore region of GFNMS based on nutrient concentration, phytoplankton community composition, chlorophyll a concentration, and net primary productivity. There was no evidence to suggest that there have been major influxes of nutrients into these areas of the sanctuary. A lack of year-round data for most indicators limited the assessment of trends during the study period.

Estuarine and Lagoon Region

Status Description: Eutrophication is suspected and may degrade some attributes of ecological integrity, but has not yet caused measurable degradation.

Rationale: Data documenting eutrophication were limited. While spikes in chlorophyll a and dinoflagellate/diatom relative abundance index and low dissolved oxygen occurred in some years, this was generally sporadic and did not suggest widespread eutrophication throughout the study period, and no signs of negative effects on ecological integrity were detected. However, Tomales Bay, Estero Americano, and Estero de San Antonio have been listed as impaired water bodies due to high levels of nutrients.

Question 7: Do sanctuary waters pose risks to human health and how are they changing?

Coastal and Offshore Region

Status Description: Water quality problems have caused measurable human impacts, but effects are localized and not widespread or persistent.

Rationale: The presence of biotoxins posed a threat to human health and resulted in fishery closures during the study period. In addition, swimming advisories were issued for some beaches adjacent to the sanctuary due to elevated levels of pathogenic bacteria; however, no beaches were listed as impaired water under the standards of the Clean Water Act. Mercury and PCBs were below regulatory thresholds during the study period except in 2010 and 2015, respectively. Although there were some improvements in beach water quality, worsening levels of biotoxins and fishery closures were of concern.

Estuarine and Lagoon Region

Status Description: Water quality problems have caused measurable human impacts, but effects are localized and not widespread or persistent.

Rationale: Saxitoxin exceeded thresholds in some years in Tomales Bay, but domoic acid was consistently below the detection limit. Shellfishery closures occurred regularly in Tomales Bay, primarily due to rainfall, but also as a result of norovirus, Vibrio, or saxitoxin. A norovirus outbreak linked to oysters cultured in Tomales Bay sickened 44 people in 2018–2019. Tomales Bay, Estero Americano, and Estero de San Antonio were listed as impaired bodies of water, and beach advisories were issued for Tomales Bay throughout the study period without a clear trend. Mercury contaminant levels were high for some species in Tomales Bay, and recommendations to limit consumption were issued. Data were generally unavailable for human health indicators in Estero Americano, Estero de San Antonio, and Bolinas Lagoon.

Question 8: Have recent, accelerated changes in climate altered water conditions and how are they changing?

Coastal and Offshore Region

Status Description: Climate-related changes have caused measurable but not severe degradation in some attributes of ecological integrity.

Rationale: Increased positive sea surface temperature anomalies were associated with two marine heatwave events during the study period. The marine heatwave in 2014–2016 resulted in unprecedented ecological and economic impacts. Habitat compression was high during the 2014–2016 and 2019 marine heatwaves, but there was no change in the habitat compression index during the study period. Low dissolved oxygen was observed at multiple sampling depths in multiple years, and hypoxic events were observed, typically in deeper water. Low aragonite saturation corresponding to corrosive conditions was observed, especially at deeper locations.

Estuarine and Lagoon Region

Status Description: Climate-related changes have caused measurable but not severe degradation in some attributes of ecological integrity.

Rationale: Data were only available for Tomales Bay, limiting the ability to assess this question. Sea surface temperature increased significantly during the study period, and positive anomalies were associated with marine heatwaves in 2014–2016 and 2019. Aragonite saturation increased during the study period, but was seasonally low enough to result in corrosive conditions. Stream flow into Tomales Bay decreased over time, and was lower than historical median discharge values in some years; salinity increased during the study period.

Question 9: Are other stressors, individually or in combination, affecting water quality, and how are they changing?

Coastal and Offshore Region

Status Description: Selected stressors are suspected and may degrade some attributes of ecological integrity, but have not yet caused measurable degradation.

Rationale: Microplastics were present in the sanctuary, but in lower abundance compared to more heavily developed coastal areas. Although discharges from U.S. Coast Guard vessels remained low, numerous illegal discharges into the sanctuary from cruise ships were documented during the study period. However, the volume of dredged material illegally discharged into the sanctuary decreased significantly. Vessel discharges and small oil spills were observed, but their impacts were not assessed or documented; no large spills occurred during the study period. Atmospheric emissions and illegal exhaust gas cleaning system discharges from vessels may result in harmful water quality impacts, but these have generally not been quantified in the sanctuary. It is unknown whether disruptions to natural sediment movement have affected turbidity.

Estuarine and Lagoon Region

Status Description: Selected stressors have caused measurable but not severe degradation in some attributes of ecological integrity.

Rationale: Pathogens from human and animal waste were prevalent in Tomales Bay; however, management actions have been taken to address this issue. Microplastics were detected in Tomales Bay sediments and biota, suggesting they were also present in the water column. There have been measurable improvements in sediment transport and tidal prism in Bolinas Lagoon due to restoration activities. Trend data were unavailable for most indicators, and no data for Estero Americano or Estero de San Antonio were available.

Habitat

Question 10: What is the integrity of major habitat types and how are they changing?

Coastal and Offshore Region

Status Description: Selected habitat loss or alteration has caused measurable but not severe degradation in some attributes of ecological integrity.

Rationale: There has been a significant loss of kelp canopy cover, stipe density, and understory algae and a proliferation of urchin barrens during the assessment period, resulting in a decline in habitat integrity. Sediment imbalances occurred along sandy beach habitat; however, shoreline armoring was stable during the study period. Structure-forming species within the rocky intertidal habitat were apparently stable in general. Healthy deep-sea coral and sponge habitats were documented in the sanctuary; however, sunken marine debris was also found at these sites.

Estuarine and Lagoon Region

Status Description: Selected habitat loss or alteration has caused severe degradation in some but not all attributes of ecological integrity.

Rationale: Estuarine and lagoon habitats in GFNMS remained significantly degraded compared to historic levels. There was no evidence that marsh or mudflat habitat has worsened since the last assessment, and some restoration projects have been undertaken to improve the integrity of these habitats. Anecdotal evidence suggested that Olympia oysters were low compared to historic levels. Eelgrass extent varied with no clear trend in Estero Americano and Estero de San Antonio, but may have increased at Tomales Bay (although differences in methodology preclude the full assessment of a trend); eelgrass was not present in Bolinas Lagoon, consistent with earlier surveys. More data are needed to better understand any specific quantitative changes in mudflat, marsh, and eelgrass over time and to assess the status and trends of Olympia oyster populations in all estuaries, especially Tomales Bay.

Question 11: What are contaminant concentrations in sanctuary habitats and how are they changing?

Coastal and Offshore Region

Status Description: Selected contaminants are suspected and may degrade some attributes of ecological integrity, but have not yet caused measurable degradation.

Rationale: Mercury was present in sediments and levels increased. Levels of PAHs and DDT (and its derivatives) in Dungeness crab samples were below regulatory thresholds during the study period. Mercury in Dungeness crab exceeded the state limit in 2010 and PCBs in Dungeness crab exceeded the FDA limit in 2015, but both contaminants were low throughout the remainder of the study period. Mercury, PAH, PCB, and DDT levels in Dungeness crab were stable during the study period. Tarball pollution decreased, except for one isolated event in the winter of 2015–2016.

Estuarine and Lagoon Region

Status Description: Selected contaminants have caused measurable but not severe degradation in some attributes of ecological integrity.

Rationale: There is ongoing mercury contamination in sediments and biota in the Walker Creek Delta in Tomales Bay as a result of historic mining activities in the Walker Creek watershed. Mercury levels in sediment decreased following cleanup of a key mine site, but total maximum daily load was exceeded in Walker Creek in multiple years since the cleanup. Vessel and car sinkings have occurred in the sanctuary’s estuaries, resulting in the release of fuel into sanctuary habitats, but the volume of contaminants released during these incidents is unknown. Tarballs, tar patties, and oiled wildlife were not observed on beaches in Tomales Bay or Bolinas Lagoon during the study period. There were little to no data on contaminants in Estero Americano, Estero de San Antonio, or Bolinas Lagoon.

Living Resources

Question 12: What is the status of keystone and foundation species and how is it changing?

Coastal and Offshore Region

Status Description: The status of keystone and foundation species suggests severe degradation in some but not all attributes of ecological integrity.

Rationale: Bull kelp declined significantly in the sanctuary due to a series of events, including the 2014–2016 marine heatwave and a historic imbalance within the kelp forest ecosystem. Sea star wasting syndrome led to the loss of the predators of purple urchins, e.g., sunflower and giant sea stars, allowing the purple urchin population to increase dramatically. Purple urchins thus overgrazed kelp beds, resulting in a persistent loss of bull kelp. During the 2014–2016 marine heatwave, habitat compression also occurred, resulting in a redistribution of forage species from further offshore to closer inshore. During cooler water conditions and stronger upwelling periods, the proportion of krill to less nutritious gelatinous zooplankton was high. During warmer water conditions, the proportion of krill to gelatinous zooplankton was low.

Estuarine and Lagoon Region

Status Description: The status of keystone or foundation species suggests measurable but not severe degradation in some attributes of ecological integrity.

Rationale: Eelgrass was documented in Tomales Bay, Estero Americano, and Estero de San Antonio. Anecdotal observations noted the absence of eelgrass in Bolinas Lagoon prior to and during the study period. There were dense eelgrass beds in Tomales Bay, which generally appeared to be healthy, although time series data were limited. Eelgrass wasting disease was present in Tomales Bay; its extent and impacts are unknown, but its presence is of concern.

Question 13: What is the status of other focal species and how is it changing?

Coastal and Offshore Region

Status Description: Selected focal species are at reduced levels, but recovery is possible.

Rationale: The 2014–2016 marine heatwave greatly impacted the abundance and distribution of numerous species that are neither keystone nor foundation species, but are considered important to sanctuary management for other reasons (i.e., other focal species). However, some focal species remained stable or increased during the study period. Although the relative abundance of young-of-the-year rockfish was relatively high from 2013–2016, it declined overall in the Gulf of the Farallones and Monterey Bay region during the study period. The regional abundance of white sharks increased in Central California. Humpback whale populations increased gradually on the West Coast, and their densities in GFNMS varied with krill densities. Since the 2014–2016 marine heatwave, densities of whales and krill increased slightly. In some years, habitat compression was a key driver of the distribution of forage species; this shifted the distribution of some focal species from the shelf break to the shelf, closer to shore, including humpback whales and Cassin’s auklets. Breeding populations of Brandt’s cormorant, Cassin’s auklet, and common murre increased during the study period. Encounter rates for shorebirds in the sanctuary were lower during the study period compared to historic values; encounter rates decreased for willets, although worldwide populations remained stable or increased, and encounter rates increased slightly for snowy plover. Sea palm and abalone densities declined during the 2014–2016 marine heatwave; sea palm showed signs of recovery, but abalone abundances remained very low.

Estuarine and Lagoon Region

Status Description: Selected focal species are at substantially reduced levels, and prospects for recovery are uncertain.

Rationale: Anecdotal observations suggest that Olympia oysters, a native species, were present in Tomales Bay and Bolinas Lagoon, but no information on their abundance was available. Brant are thought to be declining throughout their range, but encounter rates for brant in the sanctuary fluctuated without a clear trend during the study period. Shorebird encounter rates during the study period were lower than in previous decades, but it is unknown whether this reflects the global decline in shorebird abundance or a range shift out of the sanctuary.

Question 14: What is the status of non-indigenous species and how is it changing?

Coastal and Offshore Region

Status Description: Non-indigenous species are not suspected to be present or do not appear to affect ecological integrity (full community development and function).

Rationale: Non-indigenous species were present within the coastal and offshore region of GFNMS, and the number of non-indigenous species detected increased during the study period. However, available evidence suggests that the impacts of these species have been limited. Status and trend data, including abundance, density, and spatial distribution, were limited for most non-indigenous species of concern, and more long-term monitoring and systematic surveys are needed.

Estuarine and Lagoon Region

Status Description: Non-indigenous species have caused measurable but not severe degradation in some attributes of ecological integrity.

Rationale: Non-indigenous species remained present within the estuarine and lagoon region of GFNMS and caused measurable degradation at the local level. In particular, European green crabs in Tomales Bay and Bolinas Lagoon and non-native snails in Tomales Bay have had negative impacts on native species. The number of non-indigenous species in the sanctuary increased, but the rate of increase slowed during the study period compared to the last century. Some species, such as non-indigenous Spartina spp., declined, while others remained stable (European green crabs) or had variable or undetermined trends (snails). Data for most non-indigenous species were limited, and more long-term monitoring and systematic surveys are needed.

Question 15: What is the status of biodiversity and how is it changing?

Coastal and Offshore Region

Status Description: Selected biodiversity loss or change is suspected and may preclude full community development and function, but has not yet caused measurable degradation.

Rationale: Biodiversity was altered compared to near-pristine conditions, but was within the expected range of long-term natural variability. This is with the possible exception of range shifts and changes in species composition caused by the 2014–2016 marine heatwave, which, exacerbated by climate change, may have exceeded natural levels of variation. Benthic infauna species richness was high compared to areas near San Francisco Bay outflow areas. Rocky shore community stability was high. Kelp community indicators (fish, invertebrates, and understory species richness) varied. Forage fish species richness was high and remained stable over time. Groundfish species density was consistent with long-term means and was stable during the study period.

Estuarine and Lagoon Region

Status Description: N/A

Rationale: At the time of the assessment, there were no known comprehensive surveys of biodiversity in GFNMS estuaries. There was no apparent change in shorebird and marine mammal species richness during the study period, but these data were not sufficient to assess biodiversity for the entirety of the estuarine and lagoon region of the sanctuary.

Maritime Heritage Resources

Question 16: What is the condition of known maritime heritage resources and how is it changing?

Coastal and Offshore Region

Status Description: Selected maritime heritage resources exhibit indications of natural or human disturbance, but there appears to have been little or no reduction in aesthetic, cultural, historical, archaeological, scientific, or educational value.

Rationale: Historic sites, properties, and artifacts associated with shipwrecks and doghole ports are known to exist within GFNMS boundaries. The 2015 expansion of the sanctuary increased the number of maritime heritage resources within its boundaries. Summary findings of condition could be made for 13 of the 33 known shipwrecks; all 13 showed structural degradation. Some impacts to condition were due to physical processes, while others related to human interactions, although the latter did not appear to be significant. Two shipwrecks showed signs of fishing gear entanglement; however, neither trawling nor looting was known to have impacted any shipwrecks during the rating period. Twenty-four historic doghole port sites have been documented in or adjacent to GFNMS. No other maritime heritage properties were documented within sanctuary boundaries, though more are likely present. Expert confidence in the trend assessment was low because of limited evidence due to a lack of systematic site assessment and monitoring data.

Estuarine and Lagoon Region

Status Description: Known maritime heritage resources appear to reflect little or no unexpected natural or human disturbance.

Rationale: The one known resource, the shipwreck Oxford, located in Tomales Bay, is buried by mud, which makes both natural and anthropogenic deterioration less likely. Expert confidence was low in determining a trend because the assessment was based on one site and a single survey. Aircraft, doghole ports, and other maritime heritage resources were investigated as data indicators but no known resources were identified.