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 located 1 kilometer south of the discharge of the Palo Alto Regional Water Quality Control Plant (PARWQCP) in south San Francisco Bay, California. This report includes data collected by the U.S. Geological Survey (USGS) starting in January 2019. These data append to long-term datasets extending back to 1974. This dataset supports the City of Palo Alto’s Near-Field Receiving-Water Monitoring Program, initiated in 1994. This data release is presented as two datasets each on its own child page. The first child page contains clam tissue metals data, sediment metals data, percentage fine sediment, total organic carbon, and the salinity of the overlying water. The second child page contains clam reproduction and benthic community data. Please read the metadata file corresponding to each dataset for complete details.

Sediment particles can strongly bind metals, effectively repartitioning them from solution to a solid phase. As a result, sediments may accumulate and retain metals released to an aquatic environment. Sediment cores provide a historical record of metal inputs that can reveal anthropogenic influences (Förstner and Wittmann, 1979). Specifically, studies of sediment cores in San Francisco Bay chronicled metal inputs and suggested that legacy contamination can remain a chronic source of metals to the system owing to sediment mixing and redistribution (Hornberger and others, 1999; Van Geen and Luoma, 1999). Metals in sediments also indicate exposure levels to benthic animals through contact with, and ingestion of, bottom sediments and suspended particulate materials. However, physical and geochemical conditions of the sediment affect the biological availability of the bound metals. Assimilation of bioavailable sediment-bound metal by digestive processes and the contribution of this source of metals relative to metals in the aqueous phase are difficult to predict from sediment concentrations alone. Thus, in order to better estimate bioavailable metal exposures, the tissues of organisms may be analyzed for trace metals (Phillips and Rainbow, 1993). Different species concentrate metals to different degrees. However, if one species is analyzed consistently, the results can be used to track temporal changes in trace-element exposures at a specified location. This data release includes the sediment and tissue metal data starting in January 2019 and is presented in 13 tables as comma-separated values (.CSV) files as follows: T1_Sediment_Summary as a summary of the fine sediment, silver, aluminum, chromium, copper, iron, mercury, nickel, selenium, zinc and total organic carbon in the sediment. T2_Sediment_Metals_ICPOES provides detailed silver, aluminum, chromium, copper, iron, mercury, nickel, selenium and zinc data collected by inductively coupled plasma-optical emission spectrophotometry (ICP-OES) T3_Sediment_Hg_Se reports detailed mercury and selenium data T4_TOC reports detailed total organic carbon data from the sediment T5_Tissue_Metals reports the silver, chromium, copper, nickel, and zinc data collected from clams with the size and mass of the collected clam tissue for each sample date. T6_Tissue_Hg_Se reports the mercury and selenium data collected from clam tissue collected by size fraction and collection date. T7_QA_ICPOES_Sediment_SRM reports the standard reference material run data for certified reference standards for sediment analyzed on the ICP-OES. T8_QA_ICPOES_Tissue_SRM reports the standard reference material run data collected for certified standards for biological tissues analyzed on the ICP-OES. T9_QA_Hg_ Se reports the standard reference materials run for mercury and selenium data T10_QA_Spike_Recovery reports the spike recovery runs for the ICP-OES T11_QA_ICPOES_Blanks reports the procedural blanks run on the ICP-OES T12_QA_MDL_MRL reports the annual method detection limits and method reporting limits for the listed analyte T13_QA_SRM_reference_values reports the reference values for each of the reported standard reference material included in this data release

Sediment particles can strongly bind metals, effectively repartitioning them from solution to a solid phase. As a result, sediments may accumulate and retain metals released to an aquatic environment. Sediment cores provide a historical record of metal inputs that can reveal anthropogenic influences (Förstner and Wittmann, 1979). Specifically, studies of sediment cores in San Francisco Bay chronicled metal inputs and suggested that legacy contamination can remain a chronic source of metals to the system owing to sediment mixing and redistribution (Hornberger and others, 1999; Van Geen and Luoma, 1999). Metals in sediments also indicate exposure levels to benthic animals through contact with, and ingestion of, bottom sediments and suspended particulate materials. However, physical and geochemical conditions of the sediment affect the biological availability of the bound metals. Assimilation of bioavailable sediment-bound metal by digestive processes and the contribution of this source of metals relative to metals in the aqueous phase are difficult to predict from sediment concentrations alone. Thus, in order to better estimate bioavailable metal exposures, the tissues of organisms may be analyzed for trace metals (Phillips and Rainbow, 1993). Different species concentrate metals to different degrees. However, if one species is analyzed consistently, the results can be used to track temporal changes in trace-element exposures at a specified location. This data release includes the sediment and tissue metal data starting in January 2019 and is presented in 13 tables as comma-separated values (.CSV) files as follows: T1_Sediment_Summary as a summary of the fine sediment, silver, aluminum, chromium, copper, iron, mercury, nickel, selenium, zinc and total organic carbon in the sediment. T2_Sediment_Metals_ICPOES provides detailed silver, aluminum, chromium, copper, iron, mercury, nickel, selenium and zinc data collected by inductively coupled plasma-optical emission spectrophotometry (ICP-OES) T3_Sediment_Hg_Se reports detailed mercury and selenium data T4_TOC reports detailed total organic carbon data from the sediment T5_Tissue_Metals reports the silver, chromium, copper, nickel, and zinc data collected from clams with the size and mass of the collected clam tissue for each sample date. T6_Tissue_Hg_Se reports the mercury and selenium data collected from clam tissue collected by size fraction and collection date. T7_QA_ICPOES_Sediment_SRM reports the standard reference material run data for certified reference standards for sediment analyzed on the ICP-OES. T8_QA_ICPOES_Tissue_SRM reports the standard reference material run data collected for certified standards for biological tissues analyzed on the ICP-OES. T9_QA_Hg_ Se reports the standard reference materials run for mercury and selenium data T10_QA_Spike_Recovery reports the spike recovery runs for the ICP-OES T11_QA_ICPOES_Blanks reports the procedural blanks run on the ICP-OES T12_QA_MDL_MRL reports the annual method detection limits and method reporting limits for the listed analyte T13_QA_SRM_reference_values reports the reference values for each of the reported standard reference material included in this data release

Determining spatial distributions and temporal trends in trace metals in sediments and benthic organisms is common practice for monitoring environmental contamination. These data can be the basis for assessing metal exposure, the potential for adverse biological effects, and the response to regulatory or management actions (Suter, 2001). Another common method of environmental monitoring is to examine the community structure of sediment-dwelling benthic organisms (Simon, 2002). Spatial and temporal changes in community structure reflect the integrated response of resident species to environmental conditions, although the underlying cause(s) for the response may be difficult to identify and quantify. Together, measurements of metal exposure and biological response can provide a more complete view of anthropogenic disturbances and the associated effects on ecosystem health. Despite the complexities inherent in monitoring natural systems, the adopted approach has been effective in relating changes in near-field contamination to changes in reproductive activity of a clam (Hornberger and others, 2000) and in benthic community structure (Kennish, 1998). This study, with its basis in historical data, provides a rare multi-decadal context within which future environmental changes can be assessed.

Determining spatial distributions and temporal trends in trace metals in sediments and benthic organisms is common practice for monitoring environmental contamination. These data can be the basis for assessing metal exposure, the potential for adverse biological effects, and the response to regulatory or management actions (Suter, 2001). Another common method of environmental monitoring is to examine the community structure of sediment-dwelling benthic organisms (Simon, 2002). Spatial and temporal changes in community structure reflect the integrated response of resident species to environmental conditions, although the underlying cause(s) for the response may be difficult to identify and quantify. Together, measurements of metal exposure and biological response can provide a more complete view of anthropogenic disturbances and the associated effects on ecosystem health. Despite the complexities inherent in monitoring natural systems, the adopted approach has been effective in relating changes in near-field contamination to changes in reproductive activity of a clam (Hornberger and others, 2000) and in benthic community structure (Kennish, 1998). This study, with its basis in historical data, provides a rare multi-decadal context within which future environmental changes can be assessed.

These data were collected to evaluate the best measures of the effect of contaminants on the biota to be used as part of the National Status and Trends Program. Sediment and benthic samples were collected in coastal waters around San Francisco Bay, specifically from the Russian River to Santa Cruz. The samples were collected from November 1, 1986 to February 27, 1987. Each sample was tested for trace metal and organic compound concentrations, organic carbon and texture. The originator's data are in Microsoft Excel spreadsheet submitted by Dr. Edward Long from NOS/CEAB. They are documented in the NOAA technical memorandum nos OMA 45 (1989) titled "An Evaluation of Candidate Measures of Biological Effects for the National Status and Trends Program".

As a component of the ecological assessment for the Carson River Mercury Site, EPA conducted a survey of benthic macroinvertebrates to evaluate the potential adverse effects of mercury in surface water and sediment of the Carson River. Measures of benthic community response to mercury contamination derived from the benthic survey are presented in this the EcoRisk Assessment, Appendix C. A characterization of the existing environment at the sampling locations-including the habitat characteristics, fish and wildlife populations, and surrounding land use. Rapid BioAssessment Protocol II (RBP) involves the standardized collection, enumeration, and identification of major benthic taxa to the family level in riffle/run habitats. Standard data sheets are used to record results at each sampling. location. Collections are compared to a reference location, and an evaluation is made as to the impairment, or lack thereof, of the benthic community from stressors within the watershed. The biological condition of the community can be ranked according to three categories of impact: nonimpaired, moderately impaired, or severely impaired, where the degree of impairment implies less than optimal community structure, the loss of intolerant species, and dominance by a few tolerant taxa compared to background. RBP II also involves assessment of habitat characteristics such as stream flow, bottom conditions, and riparian vegetation. In addition, standard water quality parameters such as dissolved oxygen, temperature, pH, conductivity, color, and turbidity are determined. The RBP II was conducted on August 17 and 18, 1994 during a period of drought.

As a component of the ecological assessment for the Carson River Mercury Site, EPA conducted a survey of benthic macroinvertebrates to evaluate the potential adverse effects of mercury in surface water and sediment of the Carson River. Measures of benthic community response to mercury contamination derived from the benthic survey are presented in this the EcoRisk Assessment, Appendix C. A characterization of the existing environment at the sampling locations-including the habitat characteristics, fish and wildlife populations, and surrounding land use. Rapid BioAssessment Protocol II (RBP) involves the standardized collection, enumeration, and identification of major benthic taxa to the family level in riffle/run habitats. Standard data sheets are used to record results at each sampling. location. Collections are compared to a reference location, and an evaluation is made as to the impairment, or lack thereof, of the benthic community from stressors within the watershed. The biological condition of the community can be ranked according to three categories of impact: nonimpaired, moderately impaired, or severely impaired, where the degree of impairment implies less than optimal community structure, the loss of intolerant species, and dominance by a few tolerant taxa compared to background. RBP II also involves assessment of habitat characteristics such as stream flow, bottom conditions, and riparian vegetation. In addition, standard water quality parameters such as dissolved oxygen, temperature, pH, conductivity, color, and turbidity are determined. The RBP II was conducted on August 17 and 18, 1994 during a period of drought.

As a component of the ecological assessment for the Carson River Mercury Site, EPA conducted a survey of benthic macroinvertebrates to evaluate the potential adverse effects of mercury in surface water and sediment of the Carson River. Measures of benthic community response to mercury contamination derived from the benthic survey are presented in this the EcoRisk Assessment, Appendix C. A characterization of the existing environment at the sampling locations-including the habitat characteristics, fish and wildlife populations, and surrounding land use. Rapid BioAssessment Protocol II (RBP) involves the standardized collection, enumeration, and identification of major benthic taxa to the family level in riffle/run habitats. Standard data sheets are used to record results at each sampling. location. Collections are compared to a reference location, and an evaluation is made as to the impairment, or lack thereof, of the benthic community from stressors within the watershed. The biological condition of the community can be ranked according to three categories of impact: nonimpaired, moderately impaired, or severely impaired, where the degree of impairment implies less than optimal community structure, the loss of intolerant species, and dominance by a few tolerant taxa compared to background. RBP II also involves assessment of habitat characteristics such as stream flow, bottom conditions, and riparian vegetation. In addition, standard water quality parameters such as dissolved oxygen, temperature, pH, conductivity, color, and turbidity are determined. The RBP II was conducted on August 17 and 18, 1994 during a period of drought.

This data release provides the measurement of anthropogenic metals and other elements in sediments of a core obtained off San Francisquito Creek in South San Francisco Bay.