Geology topics

Research about South San Francisco Bay

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

At least 19 recordsLinked to original sources

USGS2025

Multi-scale spectroscopy to map intertidal microbial biofilm community and trait diversity

Intertidal microbial biofilms, or microphytobenthos, support estuarine biogeochemical cycling, the physical stability of mudflats, and food webs, particularly those of migratory shorebirds. Photosynthetic biofilms dominated by diatoms, cyanobacteria, and chlorophytes represent a significant fraction of biofilm biomass and contain pigments that can be detected with remote sensing. These diverse biofilm community types vary in indicator pigments and functional traits related to biogeochemical cycling and nutritional quality. We modeled and mapped spatial variation in intertidal biofilm distribution, quantity, diversity, and functional traits using multi-scale spectroscopic data collected within southern San Francisco Bay, California, USA (South SFB). We developed a new biofilm index (B-index) from 5 mm HySpex spectra to detect biofilm presence. We developed single and multiple response partial least squares regression (PLS) models of chlorophyll -a (chl -a ; biomass indicator), indicator pigments: fucoxanthin and diadinoxanthin (diatoms), zeaxanthin (cyanobacteria), and chl -b (chlorophytes), and functional traits: carbohydrates, lipids, and total organic carbon from paired in situ biofilm data and field spectra. The B-index and PLS models were scaled to South SFB with a 3.7 m AVIRIS-NG hyperspectral image. The model %RMSE calculated from AVIRIS-NG test samples ranged from 12.7% for chl -a to 49% for chl -b ; for six of the eight models, %RMSE was 23% or below. Mapped community types differed in mapped traits, with average lipid concentrations three times higher in areas indicated as diatoms compared to other groups. Available maps depict for the first time the spatial variation of an important shorebird food resource and inform the contribution of intertidal biofilm in carbon and nutrient cycling.

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USGS2023

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—2020

Trace-metal concentrations in sediment and in the clam Limecola petalum (World Register of Marine Species, 2020; formerly reported as Macoma balthica and M. petalum ), clam reproductive activity, and benthic macroinvertebrate community structure were investigated in a mudflat 1 kilometer (km) south of the discharge of the Palo Alto Regional Water Quality Control Plant (PARWQCP) in south San Francisco Bay, California. This report includes the data collected by the U.S. Geological Survey (USGS) for January 2020–December 2020 (Cain and others, 2022). These data append to long-term datasets extending back to 1974. A major focus of the report is an integrated description of the 2020 data within the context of the longer, multidecadal dataset. This dataset supports the City of Palo Alto’s Near-Field Receiving- Water Monitoring Program, initiated in 1994. Silver and copper contamination substantially decreased 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 in surface sediments have continued to decrease, although more slowly. For example, from 1994 to 2020, the minimum annual mean silver concentration—0.20 milligram per kilogram (mg/kg)—was observed in multiple years. In 2020, silver concentrations ranged from 0.18 to 0.28 mg/kg. These concentrations are 2 to 3 times higher than the regional background concentration. Presently (2020), sediment-copper concentrations appear to be near the regional background level. Over the same period (1994–2020), sedimentary iron and zinc exhibited modest decreases. Sedimentary aluminum, chromium, mercury, nickel, and selenium have not exhibited any trend. Since 1994, silver and copper concentrations in L. petalum have varied seasonally, apparently in response to a combination of site-specific metal exposures and cyclic growth and reproduction, as reported previously. Seasonal patterns for other elements, including chromium, mercury, nickel, selenium, and zinc, generally were similar in timing and magnitude as those for silver and copper. Downward trends in the silver and zinc concentrations in L. petalum during 1994–2020 were evident and appeared to be related to the general physiological condition of the clam, indicated by a condition index. Biological effects of elevated silver and copper contamination at the Palo Alto site have been interpreted from data collected during and after the recession of these contaminants. Concentrations of both elements in the soft tissues of L. petalum decreased with sedimentary copper and silver. This pattern was associated with changes in the reproductive activity of L. petalum , as well as the structure of the benthic invertebrate community. Reproductive activity of L. petalum increased as metal concentrations in L. petalum decreased (Hornberger and others, 2000), and presently is stable with almost all animals initiating reproduction in the fall and spawning the following spring. Analyses of the benthic community structure indicate that the infaunal invertebrate community has shifted from one dominated by several opportunistic species when silver and copper exposures were highest to one in which the species abundance is more evenly distributed, a pattern that indicates a more stable community that is subjected to fewer stressors. Importantly, this long-term change is unrelated to other metals and other measured environmental factors, including salinity and sediment composition. 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 decrease in dominance coincident with the decrease in metals. Both species had short-lived rebounds in abundance in 2008, 2009, and 2010 and showed signs of increasing abundance in 2020. 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 from 2011 to 2012 and returned to pre-2011 numbers in 2020. The reproductive mode of most species that were present in 2020 was indicative of species that were capable of movement 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 2020 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, those that have pelagic larvae that must survive landing on the sediment, and those that brood their young. The long-term recovery observed after the 1970s can be ascribed to the decrease in sediment pollutants.

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USGS2023

Successful hindcast of 7 years of mud morphodynamics influenced by salt pond restoration in south San Francisco Bay

Alviso Slough in South San Francisco Bay has been experiencing restoration of adjacent former salt-production ponds into muted tidal ponds, tidal ponds, and salt marsh. As a result, tidal prism through Alviso Slough has increased and mercury-contaminated sediment has been remobilized. We developed a 2D, high-resolution, process-based model (Delft3D FM-wave) to hindcast observed morpho-dynamic developments and to investigate associated sediment flux in the slough and pond system. Our results contrastingly demonstrate that a successful hindcast of the observed morphodynamic trend is made while reproducing observed intratidal suspended sediment concentrations in Alviso Slough remains a challenge. Our explanation is that the model is able to capture spatial gradients in the tide-residual sediment transports as the result of the large-scale management actions in the system, i.e., the opening of the salt ponds. These tide-residual processes are generally difficult to measure over an entire domain, but are very relevant to model the morphodynamic development. Our model provides a promising tool to trace eroding contaminated sediments to the benefit of restoration project managers and to support planning and design phases of adaptive management measures.

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USGS2021

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—2019

Trace-metal concentrations in sediment and in the clam Limecola petalum (formerly reported as Macoma balthica and M. petalum ), 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 the U.S. Geological Survey (USGS) for the period January 2019 to December 2019. These data append to long-term datasets extending back to 1974. A major focus of the report is an integrated description of the 2019 data within the context of the longer, multidecadal 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 contamination 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 in surface sediments have continued to decrease, although more slowly. Silver appears to have stabilized at concentrations about twice the regional background concentration. Presently, sediment copper concentrations appear to be near the regional background level. Over the same period (1994–2019), sedimentary iron and zinc also exhibited modest declines. Sedimentary aluminum, chromium, mercury, nickel, and selenium have not exhibited any trend. Since 1994, concentrations of silver and copper in L. petalum have varied seasonally, apparently in response to a combination of site-specific metal exposures and cyclic growth and reproduction, as reported previously. Seasonal patterns for other elements, including chromium, mercury, nickel, selenium, and zinc, were generally similar in timing and magnitude as those for silver and copper. The annual growth and reproductive cycle explained a small amount of the variance in annual silver and zinc tissue metal concentrations. However, interannual trends are not apparent for any element. Biological effects of elevated silver and copper contamination at the Palo Alto site have been interpreted from data collected during and after the recession of these contaminants. Concentrations of both elements in the soft tissues of L. petalum declined with sedimentary copper and silver. This pattern was associated with changes in the reproductive activity of L. petalum , as well as the structure of the benthic invertebrate community. Reproductive activity of L. petalum increased as metal concentrations in L. petalum declined and presently is stable with almost all animals initiating reproduction in the fall and spawning the following spring. Analyses of the benthic community structure indicate that the infaunal invertebrate community has shifted from one dominated by several opportunistic species when silver and copper exposures were highest to one in which the species abundance is more evenly distributed, a pattern that indicates a more stable community that is subjected to fewer stressors. Importantly, this long-term change is unrelated to other metals and other measured environmental factors, including salinity and sediment composition. 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 2019. 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 2019. 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 L. petalum . However, within two months of this event, animals returned to the mudflat. The resilience of the community suggested that the disturbance was not caused by a persistent toxin or anoxia. The reproductive mode of most species that were present in 2019 was indicative 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 2019 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, those that 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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USGS2020

Establishing Forster’s Tern ( Sterna forsteri ) nesting sites at pond A16 using social attraction for the South Bay Salt Pond restoration project

Forster’s terns ( Sterna forsteri ), historically one of the most numerous colonial-breeding waterbirds in South San Francisco Bay, California, have experienced recent decreases in the number of nesting colonies and overall breeding population size. The South Bay Salt Pond Restoration Project aims to restore 50–90 percent of former salt evaporation ponds to tidal marsh habitat in South San Francisco Bay. During phase 1 of the South Bay Salt Pond Restoration Project, the breaching of several pond levees to begin the process of tidal marsh restoration inundated island nesting habitat that had been used by Forster’s terns, American avocets ( Recurvirostra americana ), and other waterbirds. Additional nesting habitat could be lost as more managed ponds are converted to tidal marsh in the future. To address this issue, the South Bay Salt Pond Restoration Project organized the construction of new nesting islands in managed ponds that will not be restored to tidal marsh, thereby providing enduring island nesting habitat for waterbirds. In 2012, 16 new islands were constructed in Pond A16 in the Alviso complex of the Don Edwards San Francisco Bay National Wildlife Refuge, which increased the number of islands in this pond from 4 to 20. However, despite a long history of nesting on the four islands in Pond A16 before the 2012 construction activities, no Forster’s terns have nested in Pond A16 during the 7-year period (2012–18) after island construction. During the 2017 and 2019 breeding seasons, we used social attraction measures (decoys and colony call playback systems) to attract Forster’s terns to islands within Pond A16 to re-establish nesting colonies. We maintained these systems from March through August in each year. To evaluate the effect of these social attraction measures, we completed surveys (between April and August) where we recorded the number and location of all Forster’s terns and other waterbirds using Pond A16, and we monitored waterbird nests. We compared bird survey and nest monitoring data collected in 2017 and 2019 to data collected in 2015 and 2016, prior to the implementation of social attraction measures, allowing for direct evaluation of the effect of social attraction efforts on Forster’s terns. To increase the visibility and stakeholder involvement of this project, we engaged in multiple outreach activities in 2017, 2019, and 2020, including the development of a project website and educational video; publication of popular articles in 2017 and 2020; the development of outreach materials describing the project to the general public; and public presentations to relay findings to managers, stakeholders, and the general public. The relative abundance of Forster’s terns in Pond A16, after adjusting for the overall South San Francisco Bay breeding population each year, was higher during the nesting period in 2017 and 2019 (when social attraction was used) than in 2015 and 2016 (before social attraction was used). Furthermore, more Forster’s terns were observed during the pre-nesting and nesting periods in the areas of Pond A16 where decoys and call systems were deployed. Although no Forster’s tern nests were observed in Pond A16 before social attraction was implemented (2015, 2016), or during the first-year social attraction was implemented (2017), 35 Forster’s tern nests were recorded during the second year of social attraction implementation in 2019. These 35 nests represent a re-establishment of a Forster’s tern nesting colony to Pond A16 for the first time in 8 years. As social attraction efforts often benefit from multiple years of decoy and call system deployment, results from 2017 and 2019 suggest that continued implementation of social attraction measures could help to ensure Forster’s tern breeding colonies persist in Pond A16 and other areas of South San Francisco Bay.

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USGS2019

Slough evolution and legacy mercury remobilization induced by wetland restoration in South San Francisco Bay

Coastal wetlands have a long history of degradation and destruction due to human development. Now recognized as one of the most productive ecosystems in the world, substantial efforts are being made to restore this critical habitat. While wetland restoration efforts are generally viewed as beneficial in terms of providing wildlife habitat and flood control, they are often accompanied by dramatic physical and chemical changes that may result in unintended consequences, which are rarely studied. Alviso Slough, a tidal slough in South San Francisco Bay, California, is the site of an ongoing effort to restore former salt-production ponds to intertidal marsh habitat. Restoration is complicated by the fact that (1) the ponds undergoing restoration are severely subsided and (2) subsurface sediments within the slough and surrounding ponds are contaminated with legacy mercury deposits. Due to concerns regarding mercury remobilization, restoration has proceeded in a cautious, methodical manner. To assess the amount of legacy mercury remobilized since restoration began, we developed a technique of combining high-resolution, biannual measurements of bathymetric scour with mercury concentration measurements from sediment cores. We estimate that 52 kg (±3) of mercury was remobilized in the 6 years since restoration began. Net bathymetric change analyses revealed seasonal trends of peak erosion during the winter months and little to no net change during summer months. Our analyses provide crucial insight on the spatial and temporal scales of geomorphic evolution within a tidal slough resulting from both natural (seasonal) variability and restoration actions. The technique presented here could be applied to other study sites and various sediment-associated contaminants of concern to aid in the design and management of restoration projects aiming to minimize negative impacts from legacy contaminants.

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USGS2018

Phase 1 studies summary of major findings of the South Bay Salt Pond Restoration Project, South San Francisco Bay, California

Executive Summary The South Bay Salt Pond Restoration Project (Project) is one of the largest restoration efforts in the United States. It is located in South San Francisco Bay of California. It is unique not only for its size—more than 15,000 acres—but also for its location adjacent to one of the nation’s largest urban areas, home to more than 4 million people (Alameda, Santa Clara, and San Mateo Counties). The Project is intended to restore and enhance wetlands in South San Francisco Bay while providing for flood management, wildlife-oriented public access, and recreation. Restoration goals of the project are to provide a mosaic of saltmarsh habitat to benefit marsh species and managed ponds to benefit waterbirds, throughout 3 complexes and 54 former salt ponds. Although much is known about the project area, significant uncertainties remain with a project of this geographic and temporal scale of an estimated 50 years to complete the restoration. For example, in order to convert anywhere from 50 to 90 percent of the existing managed ponds to saltmarsh habitat, conservation managers first enhance the habitat of managed ponds in order to increase use by waterbirds, and provide migratory, wintering, and nesting habitat for more than 90 species of waterbirds. Project managers have concluded that the best way to address these uncertainties is to carefully implement the project in phases and learn from the outcome of each phase. The Adaptive Management Plan (AMP) identifies specific restoration targets for multiple aspects of the Project and defines triggers that would necessitate some type of management action if a particular aspect is trending negatively. U.S. Geological Survey (USGS) biologist Laura Valoppi served as the project Lead Scientist and oversaw implementation of the AMP in coordination with other members of the Project Management Team (PMT), comprised of representatives from the California State Coastal Conservancy, California Department of Fish and Wildlife, the Santa Clara Valley Water District, the U.S. Army Corps of Engineers, and the U.S. Fish and Wildlife Service. To implement the AMP, the PMT have selected and funded applied studies and monitoring projects to address key uncertainties. This information is used by the PMT to make decisions about current management of the project area and future restoration actions in order to meet project. This document summarizes the major scientific findings from studies conducted from 2009 to 2016, as part of the science program that was conducted in conjunction with Phase 1 restoration and management actions. Additionally, this report summarizes the management response to the study results under the guidance of the AMP framework and provides a list of suggested studies to be conducted in “Phase 2–A scorecard summarizing the Project’s progress toward meeting the AMP goals for a range of Project objectives.” The scoring to date indicates that the Project is meeting or exceeding expectations for sediment accretion and western snowy plover ( Charadrius alexandrinus nivosus ) recovery. There is uncertainty with respect to objectives for California gulls ( Larus californicus ), California least tern ( Sternula antillarum ), steelhead trout ( Oncorhynchus mykiss ), and regulatory water quality objectives. Water quality and algal blooms, specifically of the managed ponds, is indicated as trending negative. However, the vast majority of objectives are trending positive, including increased abundance for a number of bird guilds, increasing marsh habitat, maintenance of mudflats, visitor experience, estuarine fish numbers, and special-status marsh species numbers.

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USGS2018

Trends and habitat associations of waterbirds using the South Bay Salt Pond Restoration Project, San Francisco Bay, California

Executive Summary The aim of the South Bay Salt Pond Restoration Project (hereinafter “Project”) is to restore 50–90 percent of former salt evaporation ponds to tidal marsh in San Francisco Bay (SFB). However, hundreds of thousands of waterbirds use these ponds over winter and during fall and spring migration. To ensure that existing waterbird populations are supported while tidal marsh is restored in the Project area, managers plan to enhance the habitat suitability of ponds by adding islands and berms to change pond topography, manipulating water salinity and depth, and selecting appropriate ponds to maintain for birds. To help inform these actions, we used 13 years of monthly (October–April) bird abundance data from Project ponds to (1) assess trends in waterbird abundance since the inception of the Project, and (2) evaluate which pond habitat characteristics were associated with highest abundances of different avian guilds and species. For comparison, we also evaluated waterbird abundance trends in active salt production ponds using 10 years of monthly survey data. We assessed bird guild and species abundance trends through time, and created separate trend curves for Project and salt production ponds using data from every pond that was counted in a year. We divided abundance data into three seasons—fall (October–November), winter (December–February), and spring (March–April). We used the resulting curves to assess which periods had the highest bird abundance and to identify increasing or decreasing trends for each guild and species.

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USGS2018

California gull (Larus californicus) space use and timing of movements in relation to landfills and breeding colonies

Expanding gull (Laridae) populations throughout the world have been attributed to the availability of anthropogenic food subsidies. The influence of landfills on California Gull ( Larus californicus ) space use and the timing of their movements was evaluated in San Francisco Bay, California, USA. Using radio telemetry, 108 California Gulls were tracked, > 7,000 locations were recorded, and > 1 million detections were obtained at automated logger systems placed at the two main landfills and three major breeding colonies. Population home range (31-35 km 2 ) and core use areas (2-3 km 2 ) overlapped landfills and colonies, and expanded after breeding. California Gull attendance at landfills (1.6-19.0 km from colonies) increased throughout breeding and post-breeding, whereas attendance at colonies was low during pre-breeding (20%-40% per day), increased during breeding (60%-80% per day), and declined into and during post-breeding (< 20% per day). California Gull attendance at landfills was greatest when garbage was delivered from 06:00 hr in the morning until 18:00 hr at night. In contrast, California Gull attendance at colonies during breeding was greater at night from 20:00 hr to 05:00 hr (50%-70% per hr) than during the day from 06:00 hr to 18:00 hr (30%-40% per hr). Landfills played a predominant role in California Gull space use and the timing of their movements in this highly urbanized estuary.

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USGS2017

Acoustic doppler velocimeter backscatter for quantification of suspended sediment concentration in South San Francisco Bay

A data set was acquired on a shallow mudflat in south San Francisco Bay that featured simultaneous, co-located optical and acoustic sensors for subsequent estimation of suspended sediment concentrations (SSC). The optical turbidity sensor output was converted to SSC via an empirical relation derived at a nearby site using bottle sample estimates of SSC. The acoustic data was obtained using an acoustic Doppler velocimeter. Backscatter and noise were combined to develop another empirical relation between the optical estimates of SSC and the relative backscatter from the acoustic velocimeter. The optical and acoustic approaches both reproduced similar general trends in the data and have merit. Some seasonal variation in the dataset was evident, with the two methods differing by greater or lesser amounts depending on which portion of the record was examined. It is hypothesized that this is the result of flocculation, affecting the two signals by different degrees, and that the significance or mechanism of the flocculation has some seasonal variability. In the earlier portion of the record (March), there is a clear difference that appears in the acoustic approach between ebb and flood periods, and this is not evident later in the record (May). The acoustic method has promise but it appears that characteristics of flocs that form and break apart may need to be accounted for to improve the power of the method. This may also be true of the optical method: both methods involve assuming that the sediment characteristics (size, size distribution, and shape) are constant

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USGS2016

Mudflat morphodynamics and the impact of sea level rise in South San Francisco Bay

Estuarine tidal mudflats form unique habitats and maintain valuable ecosystems. Historic measurements of a mudflat in San Fancsico Bay over the past 150 years suggest the development of a rather stable mudflat profile. This raises questions on its origin and governing processes as well as on the mudflats’ fate under scenarios of sea level rise and decreasing sediment supply. We developed a 1D morphodynamic profile model (Delft3D) that is able to reproduce the 2011 measured mudflat profile. The main, schematised, forcings of the model are a constant tidal cycle and constant wave action. The model shows that wave action suspends sediment that is transported landward during flood. A depositional front moves landward until landward bed levels are high enough to carry an equal amount of sediment back during ebb. This implies that, similar to observations, the critical shear stress for erosion is regularly exceeded during the tidal cycle and that modelled equilibrium conditions include high suspended sediment concentrations at the mudflat. Shear stresses are highest during low water, while shear stresses are lower than critical (and highest at the landward end) along the mudflat during high water. Scenarios of sea level rise and decreasing sediment supply drown the mudflat. In addition, the mudflat becomes more prone to channel incision because landward accumulation is hampered. This research suggests that sea level rise is a serious threat to the presence of many estuarine intertidal mudflats, adjacent salt marshes and their associated ecological values.

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USGS2016

Acoustic Doppler velocimeter backscatter for quantification of suspended sediment concentration in South San Francisco Bay, USA

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USGS2015

Model-based interpretation of sediment concentration and vertical flux measurements in a shallow estuarine environment

A one-dimensional numerical model describing tidally varying vertical mixing and settling was used to interpret sediment concentrations and vertical fluxes observed in the shoals of South San Francisco Bay by two acoustic Doppler velocimeters (ADVs) at elevations of 0.36 m and 0.72 m above bed. Measured sediment concentrations changed by up to 100 g m −3 over the semidiurnal tidal cycle. These dynamics were dominated by local resuspension and settling. Multiple particle class models suggested the existence of a class with fast settling velocities ( w s of 9.0 × 10 −4 m s −1 in spring and 5.8 × 10 −4 m s −1 in fall) and a slowly settling particle fraction ( w s of <1 × 10 −7 m s −1 in spring and 1.4 × 10 −5 m s −1 in fall). Modeled concentrations of slowly settling particles at 0.36 m were as high as 20 g m −3 during fall and varied with the spring-neap cycle while fine sediment concentrations in spring were constant around 5 g m −3 . Analysis of in situ water column floc size distributions suggested that floc properties in the lower part of the water column were most likely governed by particle-size distribution on the bed and not by coagulation, validating our multiple particle size approach. A comparison of different sediment bed models with respect to model performance, sensitivity, and identifiability suggested that the use of a sediment erosion model linear in bottom shear stress τ b ( E = M ( τ b − τ c )) was the most appropriate choice to describe the field observations when the critical shear stress τ c and the proportionality factor M were kept constant.

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USGS2014

Lateral baroclinic forcing enhances sediment transport from shallows to channel in an estuary

We investigate the dynamics governing exchange of sediment between estuarine shallows and the channel based on field measurements at eight stations spanning the interface between the channel and the extensive eastern shoals of South San Francisco Bay. The study site is characterized by longitudinally homogeneous bathymetry and a straight channel, with friction more important than the Coriolis forcing. Data were collected for 3 weeks in the winter and 4 weeks in the late summer of 2009, to capture a range of hydrologic and meteorologic conditions. The greatest sediment transport from shallows to channel occurred during a pair of strong, late-summer wind events, with westerly winds exceeding 10 m/s for more than 24 h. A combination of wind-driven barotropic return flow and lateral baroclinic circulation caused the transport. The lateral density gradient was produced by differences in temperature and suspended sediment concentration (SSC). During the wind events, SSC-induced vertical density stratification limited turbulent mixing at slack tides in the shallows, increasing the potential for two-layer exchange. The temperature- and SSC-induced lateral density gradient was comparable in strength to salinity-induced gradients in South Bay produced by seasonal freshwater inflows, but shorter in duration. In the absence of a lateral density gradient, suspended sediment flux at the channel slope was directed towards the shallows, both in winter and during summer sea breeze conditions, indicating the importance of baroclinically driven exchange to supply of sediment from the shallows to the channel in South San Francisco Bay and systems with similar bathymetry.

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USGS2014

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: 2013

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 2013 to December 2013. These data serve as the basis for the City of Palo Alto’s Near-Field Receiving Water Monitoring Program, initiated in 1994. Following significant reductions in the late 1980s, silver (Ag) and copper (Cu) concentrations in sediment and M. petalum appear to have stabilized. 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 2013, concentrations of Ag and Cu 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. In M. petalum , all observed elements showed annual maxima in January–February and minima in April, except for Zn, which was lowest in December. In sediments, annual maxima also occurred in January–February, and minima were measured in June and September. In 2013, metal concentrations in both sediments and clam tissue were among the lowest concentrations on record. This record suggests that regional-scale factors now largely control sedimentary and bioavailable concentrations of Ag and Cu, 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 the M. petalum community shows increases in reproductive activity concurrent with the decline in metal concentrations in the tissues of this organism. Reproductive activity is presently stable (2013), with almost all animals initiating reproduction in the fall and spawning the following spring. The 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. 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 2013. An unidentified disturbance occurred on the mudflat in early 2008 that resulted in the loss of the benthic animals, except for those deep-dwelling animals like Macoma petalum . Animals immediately returned to the mudflat in 2008, which was the first indication that the disturbance was not due to a persistent toxin or to anoxia. The reproductive mode of most species present in 2013 is reflective of the 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 2013 benthic community data, which show 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 animals that consume the sediment, filter feed, have pelagic larvae that must survive landing on the sediment, and brood their young. USGS scientists continue to observe the community’s response to the 2008 defaunation event because it allows them to examine the response of the community to a natural disturbance (possible causes include sediment accretion or freshwater inundation) and compare this recovery to the long-term recovery observed in the 1970s when the decline in sediment pollutants was the dominating factor.

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USGS2010

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; 2009

Results reported herein include trace element concentrations in sediment and in the clam Macoma petalum (formerly reported as Macoma balthica (Cohen and Carlton, 1995)), clam reproductive activity, and benthic macroinvertebrate community structure for a mudflat one kilometer south of the discharge of the Palo Alto Regional Water Quality Control Plant (PARWQCP) in South San Francisco Bay. This report includes data collected for the period January 2009 to December 2009 and extends a critical long-term biogeochemical record dating back to 1974. These data serve as the basis for the City of Palo Alto’s Near-Field Receiving Water Monitoring Program, initiated in 1994. In 2009, metal concentrations in both sediments and clam tissue were among the lowest concentrations on record and consistent with results observed since 1991. Following significant reductions in the late 1980s, silver (Ag) and copper (Cu) concentrations appeared to have stabilized. Annual mean concentrations have fluctuated modestly (2–4 fold) in a nondirectional manner. Data for other metals, including chromium, mercury, nickel, selenium, vanadium, and zinc, have been collected since 1994. Over this period, concentrations of these elements, which more likely reflect regional inputs and systemwide processes, have remained relatively constant, aside from typical seasonal variation that is common to all elements. Within years, the winter months (January–March) generally exhibit maximum concentrations, with a decline to annual minima in spring through fall. Mercury (Hg) in sediments and M. petalum were comparable to concentrations observed in 2008 and were generally consistent with data from previous years. Selenium (Se) concentrations in sediment varied among years and showed no sustained temporal trend. In 2009, sedimentary Se concentrations declined from the record high concentrations observed in 2008 to concentrations that were among the lowest on record. Selenium in M. petalum was unchanged from 2008. Overall, Cu and Ag concentrations in sediments and soft tissues of the clam, M. petalum , remained representative of the concentrations observed since 1991 following significant reductions in the discharge of these elements from the PARWQCP. This suggests that, as with other elements of regulatory interest, regional-scale factors now largely influence sedimentary and bioavailable concentrations of Ag and Cu. Analyses of the benthic community structure of a mudflat in South San Francisco Bay over a 36-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 the reproductive activity 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, with almost all animals initiating reproduction in the fall and spawning the following spring of most years. The community has shifted from being dominated by several opportunistic species to a community where the species are more similar in abundance, a pattern that suggests 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 and 2009. 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, with the last several years prior to 2008 showing a stable population. An unidentified disturbance occurred on the mudflat in early 2008 that resulted in the loss of the benthic animals, except for those deep-dwelling animals like Macoma petalum . Animals immediately returned to the mudflat in 2008, which was the first indication that the disturbance was not due to a persistent toxin or to anoxia. The use of functional ecology was highlighted in the 2009 benthic community data, which show that the animals that have now returned to the mudflat are those that can respond successfully to a physical, nontoxic disturbance. Today we see plenty of animals that consume the sediment, have pelagic larvae that must survive landing on the sediment, and in some cases have eggs that must survive being laid in the sediment. We continue to observe the community’s response to the defaunation event, because it allows us to examine the response of the community to a natural disturbance (possible causes include sediment accretion or freshwater inundation) and compare this recovery to the longer-term recovery we observed in the 1970s, when the decline in sediment pollutants was the dominating factor.

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USGS2007

Legacy mercury in Alviso Slough, south San Francisco Bay, California: Concentration, speciation and mobility

Mercury (Hg) is a significant contaminant in the waters, sediment and biota of San Francisco Bay, largely resulting from extensive historic regional mining activities. Alviso Slough represents one of the most mercury contaminated waterways entering south San Francisco Bay, as it is associated with the drainage of the New Almaden mercury mining district. Wetland habitat restoration of former salt manufacturing ponds adjacent to Alviso Slough is currently being planned. One management scenario being considered is a levee breach between Alviso Slough and Pond A8, which will allow reconnection of the salt pond with the tidal slough. This action is projected to increase the tidal prism within Alviso Slough and result in some degree of sediment remobilization as the main channel deepens and widens. The focus of the current study is to assess: a) the current mercury species composition and concentration in sediments within the Alviso Slough main channel and its associated fringing marsh plain, b) how much of each mercury species will be mobilized as a result of projected channel deepening and widening, and c) potential changes in inorganic reactive mercury bioavailability (for conversion to toxic methylmercury) associated with the mobilized sediment fraction. The current report details the field sampling approach and all laboratory analyses conducted, as well as provides the complete dataset associated with this project including a) a quantitative assessment of mercury speciation (total mercury, reactive mercury and methylmercury), b) estimates of the quantity of sediment and mercury mobilized based on 20-foot and 40-foot levee wall notch scenarios, and c) results from a sediment scour experiment examining the changes in the reactive mercury pool under four treatment conditions (high / low salinity and oxic / anoxic water). Ancillary sediment data also collected and reported herein include bulk density, organic content, magnetic susceptibility, percent dry weight, grain size, pH, oxidation-reduction potential, core photography, and detailed lithographic descriptions.

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USGS2004

Near-field receiving water monitoring of a benthic community near the Palo Alto Water Quality Control Plant in south San Francisco Bay: February 1974 through December 2003

Analyses of the benthic community structure of a mudflat in South San Francisco Bay over a 29-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 biosentinal clam Macoma balthica from the same area. The community has shifted from being dominated by several opportunistic species to a community where the species are more similar in abundance, a pattern that could be indicative of a more stable community that is subjected to less stress. 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. Heteromastus filiformis, a subsurface polychaete worm that lives in the sediment, consumes sediment and organic particles residing in the sediment, and reproduces by laying their eggs on or in the sediment has shown a concurrent increase in dominance. These changes in species dominance reflect a change in the community from one dominated by surface dwelling, brooding species to one with species with varying life history characteristics. Analysis of the reproductive activity of Macoma balthica shows increases in reproductive activity concurrent with the decline in metal concentrations in the tissue of this organism. Reproductive activity is presently stable with almost all animals reproducing during the two reproductive seasons (spring and fall) of most years. These findings are consistent with findings previously reported for the 1974 through 2002 period.

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