Geology topics

Research about San Francisco Bay

Source-linked reports with geographic coverage including San Francisco Bay.

At least 55 records · Page 3Linked to original sources

USGS2018

Reported investments in earthquake mitigation top $73 to $80 billion in the San Francisco Bay Area, California, since the 1989 Loma Prieta earthquake

The purpose of this report is to provide a compilation of structural retrofits and replacements of older buildings and infrastructure in the San Francisco Bay Area that have either been completed since 1989 or that are in progress as of October 2018. For the purposes of this report, all or parts of nine Bay Area counties were included: Alameda, Contra Costa, Marin, Napa, San Francisco, San Mateo, Santa Clara, Solano, and Sonoma. Santa Cruz County was not included. The compilation of 700 investments is presented as a table in the appendix. We consider this table as version 1, as we urge that those familiar with additional projects contact the report authors with information to update the table. In total, we have identified \$73 to \$80 billion in investments to retrofit or replace structures to mitigate the impacts of future San Francisco Bay Area earthquakes. These totals represent an average investment of \$2.5 to \$2.8 billion per year in retrofits and replacement of structures since 1989.

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USGS2018

Patterns, pace and processes of water-quality variability: Examples from a long-studied estuary

Environmental time series have rich information content that is invaluable for measuring and understanding changes over time and guiding policies to manage change. I extracted information from measurements of 10 water‐quality constituents in upper San Francisco Bay from 1975 to 2016, one of the longest observational records in a U.S. estuary. Changes were detected at every time scale captured by monthly sampling. Long‐term trends included increased ammonium (+53%), nitrate + nitrate (+50%), silicate (+14%), Secchi depth (+42%), and decreased chlorophyll a (Chl a ) (−74%) and suspended particulate matter (−45%). Changes at the decadal scale included abrupt shifts (Chl a , nitrate + nitrite) and oscillations between shorter trends of increase and decrease (Secchi depth, phosphate). Long‐term trends were not expressed equally across all seasons, and seasonal patterns of change varied across constituents. These examples illustrate key features of environmental variability at the land–sea interface: (1) water‐quality components change continually at time scales from months to decades; (2) patterns of seasonal, multiyear, and multidecadal change are complex and vary across constituents; (3) primary drivers of change are freshwater inflow, the master regulator of estuarine dynamics, and human activities such as river damming, water diversions, wastewater discharge, environmental policies, and species introductions; (4) extracting the full information content of time series requires multiple analyses, each revealing a different layer of insight into how changes develop over time; (5) water‐quality variability is nonstationary, so future changes cannot be forecast reliably; (6) repeated observation is an essential method of Earth system science with applications in the design and performance measures of environmental policies.

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USGS2018

Near-field receiving-water monitoring of trace metals and a benthic community near the Palo Alto Regional Water Quality Control Plant in south San Francisco Bay, California—2017

Trace-metal concentrations in sediment and in the clam Macoma petalum (formerly reported as Macoma balthica ), clam reproductive activity, and benthic macroinvertebrate community structure were investigated in a mudflat 1 kilometer south of the discharge of the Palo Alto Regional Water Quality Control Plant (PARWQCP) in south San Francisco Bay, Calif. This report includes the data collected by U.S. Geological Survey (USGS) scientists for the period January 2017 to December 2017. These append to long-term datasets extending back to 1974. A major focus of the report is an integrated description of the 2017 data within the context of the longer, multi-decadal dataset. This dataset supports the City of Palo Alto’s Near-Field Receiving Water Monitoring Program, initiated in 1994. Significant reductions in silver and copper concentrations in sediment and M. petalum occurred at the site in the 1980s following the implementation by PARWQCP of advanced wastewater treatment and source control measures. Since the 1990s, concentrations of these elements appear to have stabilized at concentrations somewhat above silver (Ag) or near copper (Cu) regional background concentrations. Data for other metals, including chromium (Cr), mercury (Hg), nickel (Ni), selenium (Se), and zinc (Zn), have been collected since 1994. Over this period, concentrations of these elements have remained relatively constant, aside from seasonal variation that is common to all elements. In 2017, concentrations of silver and copper in M. petalum varied seasonally in response to a combination of site-specific metal exposures and annual growth and reproduction, as reported previously. Seasonal patterns for other elements, including Cr, Ni, Zn, Hg, and Se, were generally similar in timing and magnitude as those for Ag and Cu. This record suggests that legacy contamination and regional-scale factors now largely control sedimentary and bioavailable concentrations of silver and copper, as well as other elements of regulatory interest, at the Palo Alto site. Analyses of the benthic community structure of a mudflat in south San Francisco Bay over a 40-year period show that changes in the community have occurred concurrent with reduced concentrations of metals in the sediment and in the tissues of the biosentinel clam, M. petalum , from the same area. Analysis of M. petalum shows increases in reproductive activity concurrent with the decline in metal concentrations in the tissues of this organism. Reproductive activity is presently stable (2017), with almost all animals initiating reproduction in the fall and spawning the following spring. The entire infaunal community has shifted from being dominated by several opportunistic species to a community where the species are more similar in abundance, a pattern that indicates a more stable community that is subjected to fewer stressors. In addition, two of the opportunistic species ( Ampelisca abdita and Streblospio benedicti ) that brood their young and live on the surface of the sediment in tubes have shown a continual decline in dominance coincident with the decline in metals; both species had short-lived rebounds in abundance in 2008, 2009, and 2010 and showed signs of increasing abundance in 2017. Heteromastus filiformis (a subsurface polychaete worm that lives in the sediment, consumes sediment and organic particles residing in the sediment, and reproduces by laying its eggs on or in the sediment) showed a concurrent increase in dominance and, in the last several years before 2008, showed a stable population. H. filiformis abundance increased slightly in 2011–2012 and returned to pre-2011 numbers in 2017. An unidentified disturbance occurred on the mudflat in early 2008 that resulted in the loss of the benthic animals, except for deep-dwelling animals like M. petalum . However, within two months of this event animals returned to the mudflat. The resilience of the community suggested that the disturbance was not due to a persistent toxin or anoxia. The reproductive mode of most species that were present in 2017 is reflective of species that were available either as pelagic larvae or as mobile adults. Although oviparous species were lower in number in this group, the authors hypothesize that these species will return slowly as more species move back into the area. The use of functional ecology was highlighted in the 2017 benthic community data, which showed that the animals that have now returned to the mudflat are those that can respond successfully to a physical, nontoxic disturbance. Today, community data show a mix of species that consume the sediment, or filter feed, have pelagic larvae that must survive landing on the sediment, and those that brood their young. USGS scientists view the 2008 disturbance event as a response by the infaunal community to an episodic natural stressor (possibly sediment accretion or a pulse of freshwater), in contrast to the long-term recovery from metal contamination. We will compare this recovery to the long-term recovery observed after the 1970s when the decline in sediment pollutants was the dominating factor.

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USGS2018

Status of selenium in south San Francisco Bay—A basis for modeling potential guidelines to meet National tissue criteria for fish and a proposed wildlife criterion for birds

The U.S. Environmental Protection Agency (EPA) proposed Aquatic Life and AquaticDependent Wildlife Criteria for Selenium (Se) in California’s San Francisco Bay and Delta (Bay-Delta) in June 2016. Here we apply the same modeling methodology—Ecosystem-Scale Selenium Modeling— to an assessment of conditions and documentation of food webs of south San Francisco Bay (South Bay) as an exploratory framework in support of site-specific Se criteria development. Long-term datasets contribute to the basis for modeling, especially the 21-year collection of the clam Macoma petalum from a mudflat at the lower end of South Bay (Lower South Bay). As such, this is a working document that may serve as a basis to establish an understanding of the specifics of Se biodynamics within the estuary and reduce uncertainties about how to protect it. This approach brings together the main factors involved in toxicity: likelihood of high exposure, inherent species sensitivity, and the behavioral ecology (for example, demographics and life history) of an organism in terms of susceptibility to a reproductive toxicant. Species sensitivity is represented here by use of the EPA’s current national tissue Se criterion for fish or that proposed to protect the eggs of aquatic birds for the Bay-Delta (U.S. Environmental Protection Agency, 2016a, 2016b, 2016c). This report also strives to bring together findings and field data across a body of literature for South Bay to provide an integrative assessment. We find an assemblage of site-specific conditions that could affect modeling: associated urban processes such as discharges from municipal wastewater treatment plants and drainage from mercury (Hg) mining and limestone extraction are sources of Se that characterize the Lower South Bay as the location of interest for Se exposure; • hydrodynamics are lagoon-like (that is, less flushing), which sustains elevated nutrients and phytoplankton blooms; • managed freshwater sources are a major hydrodynamic component; • birds, in addition to fish, are prominent predators in South Bay; • wetland restoration has recently intervened to play a significant role in ecosystem function that may include uptake of both Hg and Se; • the dietary food web of surficial-sediment to M. petalum is important because of the dominance of this clam species and its elevated Se bioaccumulation potential compared to other local food webs; and 2 • maximal Se concentrations may be limited by transitory or annually renewed food webs (for example, migratory shorebirds and decimation of clams from marshes). We also find that the constructed mechanistic model: • spatially connects to the Palo Alto mudflat site because of data availability; • accurately predicts average observed Se concentrations in M. petalum and in predator species of fish and birds; and • is able to bracket a range of potential protective water-column Se concentrations specific to predator species based on the EPA’s national Se criterion for whole-body fish tissue and a proposed site-specific criterion for bird eggs in the Bay-Delta.

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USGS2018

Three-dimensional modeling of ﬁne sediment transport by waves and currents in a shallow estuary

A suspended sediment transport model is implemented in the unstructured‐grid SUNTANS model and applied to study fine‐grained sediment transport in South San Francisco Bay. The model enables calculation of suspension of bottom sediment based on combined forcing of tidal currents and wind waves. We show that accurate results can be obtained by employing two‐size classes which are representative of microflocs and macroflocs in the Bay. A key finding of the paper is that the critical calibration parameter is the ratio of the erosion of the microflocs to macroflocs from the bed. Different values of this erosion ratio are needed on the shallow shoals and deeper channels because of the different nature of the sediment dynamics in these regions. Application of a spatially variable erosion ratio and critical shear stress for erosion is shown to accurately reproduce observed suspended sediment concentration at four‐field sites located along a cross‐channel transect. The results reveal a stark contrast between the behavior of the suspended sediment concentration on the shoals and in the deep channel. Waves are shown to resuspend sediments on the shoals, although tidal and wind‐generated currents are needed to mix the thin wave‐driven suspensions into the water column. The contribution to the suspended sediment concentration in the channel by transport from the shoals is similar in magnitude to that due to local resuspension. However, the local contribution is in phase with strong bottom currents which resuspend the sediments, while the contribution from the shoals peaks during low‐water slack tide.

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USGS2018

The influence of sea level rise on the regional interdependence of coastal infrastructure

Sea level rise (SLR) is placing both immediate and long‐term pressures on coastal communities to take protective actions. Projects in the United States, and in many locations throughout the world, generally involve local jurisdictions raising the elevation of shoreline protection elements, with limited or no analysis of the feedback between shoreline management decisions and the impacts to water levels regionally. Our study examines the impact of local shoreline development on regional flood risk and considers SLR scenarios up to 1.5 m using a large‐scale numerical model, as an example, for San Francisco Bay. Here we show that measures to prevent flooding along an embayment shoreline in one location or subregion may increase inundation elsewhere in the system. The network of interactions occurs not only within subbasins of the Bay but also across the greater geographic extent from one end of the Bay to the other, and local jurisdiction may have either reciprocal relationships with or asymmetric impacts on one other. Importantly, the nature of the interaction network is seen to evolve with SLR: interactions are purely subregional at current sea level but with higher sea level (e.g., 1 m of SLR), not only do the subregional interdependencies strengthen but also regional interdependences emerge.

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USGS2018

Prey fish returned to Forster’s tern colonies suggest spatial and temporal differences in fish composition and availability

Predators sample the available prey community when foraging; thus, changes in the environment may be reflected by changes in predator diet and foraging preferences. We examined Forster’s tern ( Sterna forsteri ) prey species over an 11-year period by sampling approximately 10,000 prey fish returned to 17 breeding colonies in south San Francisco Bay, California. We compared the species composition among repeatedly-sampled colonies (≥ 4 years), using both relative species abundance and the composition of total dry mass by species. Overall, the relative abundances of prey species at seven repeatedly-sampled tern colonies were more different than would be expected by chance, with the most notable differences in relative abundance observed between geographically distant colonies. In general, Mississippi silverside ( Menidia audens ) and topsmelt silverside ( Atherinops affinis ) comprised 42% of individuals and 40% of dry fish mass over the study period. Three-spined stickleback ( Gasterosteus aculeatus ) comprised the next largest proportion of prey species by individuals (19%) but not by dry mass (6%). Five additional species each contributed ≥ 4% of total individuals collected over the study period: yellowfin goby ( Acanthogobius flavimanus ; 10%), longjaw mudsucker ( Gillichthys mirabilis ; 8%), Pacific herring ( Clupea pallasii ; 6%), northern anchovy ( Engraulis mordax ; 4%), and staghorn sculpin ( Leptocottus armatus ; 4%). At some colonies, the relative abundance and biomass of specific prey species changed over time. In general, the abundance and dry mass of silversides increased, whereas the abundance and dry mass of three-spined stickleback and longjaw mudsucker decreased. As central place foragers, Forster’s terns are limited in the distance they forage; thus, changes in the prey species returned to Forster’s tern colonies suggest that the relative availability of some fish species in the environment has changed, possibly in response to alteration of the available habitat.

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USGS2018

Continuous water-quality and suspended-sediment transport monitoring in the San Francisco Bay, California, water years 2014–15

The U.S. Geological Survey (USGS) monitors water quality and suspended-sediment transport in the San Francisco Bay (bay) as part of a multi-agency effort to address management, water supply, and ecological concerns. The San Francisco Bay area is home to millions of people, and the bay teems both with resident and with migratory wildlife, plants, and fish. Freshwater mixes with salt water in the bay, which is subject both to riverine influences (floods, droughts, managed reservoir releases and freshwater diversions) and to marine influences (tides, waves, effects of salt water). To understand this environment, the USGS, along with its partners (see “Acknowledgements”), has been monitoring the bay’s waters continuously since 1988. Several water-quality variables are of particular importance to State and Federal resource managers and are monitored at key locations throughout the bay (fig. 1). Salinity, which indicates the relative mixing of fresh and ocean waters in the bay, is derived from specific conductance measurements. Water temperature, along with salinity, affects the density of water, which controls gravity-driven circulation patterns and stratification in the water column. Turbidity, a measure of light scattered from suspended particles in the water, is used to estimate suspended-sediment concentration (SSC). Suspended sediment affects the bay in multiple ways: attenuation of sunlight in the water column, affecting phytoplankton growth; deposition on tidal marsh and intertidal mudflats, which can help sustain these habitats as sea level rises; deposition in ports and shipping channels, which can necessitate dredging; and often, adsorption of contaminants, affecting their distribution and concentrations in the environment. Dissolved oxygen concentration, essential to a healthy ecosystem and a fundamental indicator of water quality, is affected by water temperature, salinity, ecosystem metabolism, tidal currents, and wind. Tidal currents in the bay reverse four times a day, and wind direction and intensity typically vary on a daily cycle. Consequently, salinity, water temperature, SSC, and dissolved-oxygen concentration vary spatially and temporally throughout the bay. Therefore, continuous measurements are needed to observe these changes. The purpose of this fact sheet is to provide information about these variables, as well as internet links to access these continuous water-quality data collected by the USGS.

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USGS2018

Wave attenuation across a tidal marsh in San Francisco Bay

Wave attenuation is a central process in the mechanics of a healthy salt marsh. Understanding how wave attenuation varies with vegetation and hydrodynamic conditions informs models of other marsh processes that are a function of wave energy (e.g. sediment transport) and allows for the incorporation of marshes into coastal protection plans. Here, we examine the evolution of wave height across a tidal salt marsh in San Francisco Bay. Instruments were deployed along a cross-shore transect, starting on the mudflat and crossing through zones dominated by Spartina foliosa and Salicornia pacifica . This dataset is the first to quantify wave attenuation for these vegetation species, which are abundant in the intertidal zone of California estuaries. Measurements were collected in the summer and winter to assess seasonal variation in wave attenuation. Calculated drag coefficients of S. foliosa and S. pacifica were similar, indicating equal amounts of vegetation would lead to similar energy dissipation; however, S. pacifica has much greater biomass close to the bed (<20 cm) and retains biomass throughout the year, and therefore, it causes more total attenuation. S. foliosa dies back in the winter, and waves often grow across this section of the marsh. For both vegetation types, attenuation was greatest for low water depths, when the vegetation was emergent. For both seasons, attenuation rates across S. pacifica were the highest and were greater than published attenuation rates across similar ( Spartina alterniflora ) salt marshes for the comparable depths. These results can inform designs for marsh restorations and management plans in San Francisco Bay and other estuaries containing these species.

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USGS2018

Blurred lines: Multiple freshwater and marine algal toxins at the land-sea interface of San Francisco Bay, California

San Francisco Bay (SFB) is a eutrophic estuary that harbors both freshwater and marine toxigenic organisms that are responsible for harmful algal blooms. While there are few commercial fishery harvests within SFB, recreational and subsistence harvesting for shellfish is common. Coastal shellfish are monitored for domoic acid and paralytic shellfish toxins (PSTs), but within SFB there is no routine monitoring for either toxin. Dinophysis shellfish toxins (DSTs) and freshwater microcystins are also present within SFB, but not routinely monitored. Acute exposure to any of these toxin groups has severe consequences for marine organisms and humans, but chronic exposure to sub-lethal doses, or synergistic effects from multiple toxins, are poorly understood and rarely addressed. This study documents the occurrence of domoic acid and microcystins in SFB from 2011 to 2016, and identifies domoic acid, microcystins, DSTs, and PSTs in marine mussels within SFB in 2012, 2014, and 2015. At least one toxin was detected in 99% of mussel samples, and all four toxin suites were identified in 37% of mussels. The presence of these toxins in marine mussels indicates that wildlife and humans who consume them are exposed to toxins at both sub-lethal and acute levels. As such, there are potential deleterious impacts for marine organisms and humans and these effects are unlikely to be documented. These results demonstrate the need for regular monitoring of marine and freshwater toxins in SFB, and suggest that co-occurrence of multiple toxins is a potential threat in other ecosystems where freshwater and seawater mix.

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USGS2018

Estimating fluvial discharges coincident with 21st century coastal storms modeled with CoSMoS

On the open coast, flooding is largely driven by tides, storm surge, waves, and in areas near coastal inlets, the magnitude and co-occurrence of high fluvial discharges. Statistical methods are typically used to estimate the individual probability of coastal storm and fluvial discharge occurrences for use in sophisticated flood hazard models. A challenge arises when considering possible future climate changes and the relation between the intensity of extreme coastal water levels and high fluvial discharges. In this study, the Coastal Storm Modeling System (CoSMoS) is used to dynamically downscale global climate projections to local-scale storm-driven coastal water levels, including associated fluvial discharges. An efficient approach to derive 21st century projected fluvial discharges for rivers within San Francisco Bay was developed, leveraging a readily-available time-series of projected (2010 – 2100) discharge rates of the predominant river system (the “Delta”). Delta projections were used to estimate flow rates of 8 Bay rivers for the IPCC's CMIP5 RCP4.5 climate scenario. Relationships describing discharge rates, normalized by respective watershed areas, were developed and applied to projected data to generate 21st century fluvial discharge time-series for each river. Results indicate decreasing discharge rates throughout the 21 st century with the exception of extreme flows.

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USGS2018

Geology and geologic history: Overview of the geology of the San Francisco Bay region

The geology of San Francisco and the surrounding northern and central California area has played a pivotal role in the development of our understanding of Earth processes, especially the process of tectonic accretion at a continental margin and the development of transform plate margins. The Franciscan Complex, which underlies most (or perhaps all) of the City and County of San Francisco, is widely considered the "type" accretionary complex. More regionally, the Sierra Nevada, Great Valley, and Coast Ranges are often used as an illustration of the arc-forearc-accretionary prism geometry of a continental convergent margin, and the San Andreas Fault, just offshore to the west of San Francisco, serves as the prototype transform plate margin, although as illustrated below the actual geometry and geologic history is more complicated.

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USGS2018

Initial dispersal (1986-1987) of the invasive foraminifera Trochammina hadai Uchio in San Francisco Bay, California, USA

A time series of three closely-spaced data sets are used to track the early expansion of the invasive Japanese benthic foraminifera Trochammina hadai in the southern portion of San Francisco Bay known as South Bay. The species initially appeared in 1983, comprising only 1.5% of the assemblage in one of four samples that were dominated by the native species Ammonia tepida and Cribroelphidium excavatum (means = 60.2% and 33.8%, respectively). By 1986, census counts and R- andQ-mode cluster analyses document the explosive growth of the invasive as T. hadai now dominates the assemblage (mean = 42.7%;max = 88.7%)with associated declines in abundance of A. tepida (by greater than one-half; mean = 26.8%) and C. excavatum (by greater than one-third; mean = 20.6%). The invasive continued to dominant the assemblage in 1987, spreading even further to the north and south in South Bay, although its average abundance dropped slightly (~2%) as did those of A. tepida (~3%) and C. excavatum (0.4%). A rare increase in abundance of Elphidiella hannai and the appearance of numerous coastalmarine species in the central portion of the bay are thought to be the result of an incursion ofmarine waters into South Bay due to the prevalent drought conditions in 1987. Clearly, the rapid decline in abundance of the formerly dominant species A. tepida and C. excavatum in South Bay from 1983 to 1986 that continued into 1987 suggests the introduction of T. hadai in the bay severely impacted the native population.

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USGS2017

Clusters of community exposure to coastal flooding hazards based on storm and sea level rise scenarios—implications for adaptation networks in the San Francisco Bay region

Sea level is projected to rise over the coming decades, further increasing the extent of flooding hazards in coastal communities. Efforts to address potential impacts from climate-driven coastal hazards have called for collaboration among communities to strengthen the application of best practices. However, communities currently lack practical tools for identifying potential partner communities based on similar hazard exposure characteristics. This study uses statistical cluster analysis to identify similarities in community exposure to flooding hazards for a suite of sea level rise and storm scenarios. We demonstrate this approach using 63 jurisdictions in the San Francisco Bay region of California (USA) and compare 21 distinct exposure variables related to residents, employees, and structures for six hazard scenario combinations of sea level rise and storms. Results indicate that cluster analysis can provide an effective mechanism for identifying community groupings. Cluster compositions changed based on the selected societal variables and sea level rise scenarios, suggesting that a community could participate in multiple networks to target specific issues or policy interventions. The proposed clustering approach can serve as a data-driven foundation to help communities identify other communities with similar adaptation challenges and to enhance regional efforts that aim to facilitate adaptation planning and investment prioritization.

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USGS2017

Water quality measurements in San Francisco Bay by the U.S. Geological Survey, 1969–2015

The U.S. Geological Survey (USGS) maintains a place-based research program in San Francisco Bay (USA) that began in 1969 and continues, providing one of the longest records of water-quality measurements in a North American estuary. Constituents include salinity, temperature, light extinction coefficient, and concentrations of chlorophyll- a , dissolved oxygen, suspended particulate matter, nitrate, nitrite, ammonium, silicate, and phosphate. We describe the sampling program, analytical methods, structure of the data record, and how to access all measurements made from 1969 through 2015. We provide a summary of how these data have been used by USGS and other researchers to deepen understanding of how estuaries are structured and function differently from the river and ocean ecosystems they bridge.

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USGS2017

Downscaling wind and wavefields for 21st century coastal flood hazard projections in a region of complex terrain

While global climate models (GCMs) provide useful projections of near-surface wind vectors into the 21st century, resolution is not sufficient enough for use in regional wave modeling. Statistically downscaled GCM projections from Multivariate Adaptive Constructed Analogues provide daily averaged near-surface winds at an appropriate spatial resolution for wave modeling within the orographically complex region of San Francisco Bay, but greater resolution in time is needed to capture the peak of storm events. Short-duration high wind speeds, on the order of hours, are usually excluded in statistically downscaled climate models and are of key importance in wave and subsequent coastal flood modeling. Here we present a temporal downscaling approach, similar to constructed analogues, for near-surface winds suitable for use in local wave models and evaluate changes in wind and wave conditions for the 21st century. Reconstructed hindcast winds (1975–2004) recreate important extreme wind values within San Francisco Bay. A computationally efficient method for simulating wave heights over long time periods was used to screen for extreme events. Wave hindcasts show resultant maximum wave heights of 2.2 m possible within the Bay. Changes in extreme over-water wind speeds suggest contrasting trends within the different regions of San Francisco Bay, but 21th century projections show little change in the overall magnitude of extreme winds and locally generated waves.

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USGS2017

Ecosystem variability along the estuarine salinity gradient: Examples from long-term study of San Francisco Bay

The salinity gradient of estuaries plays a unique and fundamental role in structuring spatial patterns of physical properties, biota, and biogeochemical processes. We use variability along the salinity gradient of San Francisco Bay to illustrate some lessons about the diversity of spatial structures in estuaries and their variability over time. Spatial patterns of dissolved constituents (e.g., silicate) can be linear or nonlinear, depending on the relative importance of river-ocean mixing and internal sinks (diatom uptake). Particles have different spatial patterns because they accumulate in estuarine turbidity maxima formed by the combination of sinking and estuarine circulation. Some constituents have weak or no mean spatial structure along the salinity gradient, reflecting spatially distributed sources along the estuary (nitrate) or atmospheric exchanges that buffer spatial variability of ecosystem metabolism (dissolved oxygen). The density difference between freshwater and seawater establishes stratification in estuaries stronger than the thermal stratification of lakes and oceans. Stratification is strongest around the center of the salinity gradient and when river discharge is high. Spatial distributions of motile organisms are shaped by species-specific adaptations to different salinity ranges (shrimp) and by behavioral responses to environmental variability (northern anchovy). Estuarine spatial patterns change over time scales of events (intrusions of upwelled ocean water), seasons (river inflow), years (annual weather anomalies), and between eras separated by ecosystem disturbances (a species introduction). Each of these lessons is a piece in the puzzle of how estuarine ecosystems are structured and how they differ from the river and ocean ecosystems they bridge.

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USGS2017

Novel analyses of long-term data provide a scientific basis for chlorophyll-a thresholds in San Francisco Bay

San Francisco Bay (SFB), USA, is highly enriched in nitrogen and phosphorus, but has been resistant to the classic symptoms of eutrophication associated with over-production of phytoplankton . Observations in recent years suggest that this resistance may be weakening, shown by: significant increases of chlorophyll- a ( chl-a ) and decreases of dissolved oxygen (DO), common occurrences of phytoplankton taxa that can form Harmful Algal Blooms (HAB), and algal toxins in water and mussels reaching levels of concern. As a result, managers now ask: what levels of chl-a in SFB constitute tipping points of phytoplankton biomass beyond which water quality will become degraded, requiring significant nutrient reductions to avoid impairments? We analyzed data for DO, phytoplankton species composition, chl-a, and algal toxins to derive quantitative relationships between three indicators (HAB abundance, toxin concentrations, DO) and chl-a . Quantile regressions relating HAB abundance and DO to chl-a were significant, indicating SFB is at increased risk of adverse HAB and low DO levels if chl-a continues to increase. Conditional probability analysis (CPA) showed chl-a of 13 mg m −3 as a “protective” threshold below which probabilities for exceeding alert levels for HAB abundance and toxins were reduced. This threshold was similar to chl-a of 13–16 mg m −3 that would meet a SFB-wide 80% saturation Water Quality Criterion (WQC) for DO. Higher “at risk” chl-a thresholds from 25 to 40 mg m −3 corresponded to 0.5 probability of exceeding alert levels for HAB abundance, and for DO below a WQC of 5.0 mg L −1 designated for lower South Bay (LSB) and South Bay (SB). We submit these thresholds as a basis to assess eutrophication status of SFB and to inform nutrient management actions. This approach is transferrable to other estuaries to derive chl-a thresholds protective against eutrophication.

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