Habitat biogeochemistry was assessed by measuring 31 variables in sediments, porewater, and surface waters related to mercury content, organic matter, sediment characteristics, and microbial rates of sulfate reduction, iron reduction, and methanogenesis. Fifty-six composite surface (0-2 cm) sediment cores and 32 surface water samples were collected in three wetlands in the spring and summer of 2005 and 2006.

This dataset includes mercury and other constituent concentration and physical properties data for surface sediment, pore water and surface water collected as part of the South San Francisco Bay Salt Pond Restoration Phase 1 (2010 to 2018) studies. The overarching focus of these studies was to monitor mercury (Hg) biogeochemistry in both sediment and water in response to management actions associated with the conversion of former salt producing ponds to contemporary wetland habitat. The two primary management actions included the breaching of Pond A6 during December 2010, and the construction and operation of an adjustable tidal control structure (TCS) associated with the Pond A5/A7/A8 Complex beginning in June 2011. The TSC that reconnects the Complex to Alviso Slough (specifically referred to as the A8-TCS), a historically Hg contaminated waterway that represents the terminus of watershed drainage that includes the New Almaden mercury mining district. The A8-TCS consists of eight gates, each five feet wide. During the initial testing period (starting in June 2011) only one gate was opened, and the structure was closed again during the winter-spring months (from December until the following June). Over the subsequent seven years, the number of gates open was increased to three (15 feet, June 2012), to five (25 feet, September 2014), and eventually to all eight (40 feet, June 2017). Beginning in 2014 the A8-TCS was opened year-round. Field sampling occurred in both ponds and sloughs. In addition to sampling within the Complex ponds, two control ponds (A3N and A16) were also sampled. Similarly, in addition to sampling within Alviso Slough, two nearby control sloughs (Mallard Slough a.k.a Artesian Slough and Guadalupe Slough) were sampled (beginning in 2014 for Guadalupe Slough). Sediment sampling was conducted for the period of May 2010 through August 2011, which represents the period immediately prior to and immediately after the two above mentioned management actions. Additional sediment sampling was conducted in Mallard Slough exclusively during the August- September period 2011-2013, 2015, and 2017. Surface water sampling was conducted during three periods. The first period was in conjunction with the sediment sampling (May 2010 through August 2011). The second period involved a unique series of high temporal resolution sampling events conducted at a single site in mid-Alviso Slough, when water samples were collected hourly over a 25-hour period to capture the Hg dynamics associated with two full tidal cycles. A total of five such high-resolution ‘diel’ sampling events were conducted between May 2012 and February 2013, which included each of the four seasons and the annual ‘first flush’ event associated with the initiation of the 2012-13 rainy season. The third period, from February 2014 through February 2018, represents when all ponds and sloughs were again sampled (akin to the first period). This third period also represents when the A8-TCS was sequentially opened from 15 feet (3 gates open) to 40 feet (all 8 gates open), and when the A8-TCS management transitioned from being closed during the winter months to being opened year-round, beginning in 2014. This data release includes five data tables given both as Excel (*.xlxs) and machine readable 'comma-separated values' format (*.csv): 1) ‘SBSP.Data.Dictionary_2010-18’, the Data Dictionary, which provides definitions and details related to the other four data tables and includes analytical methods citations; 2) ‘SBSP.SED_2010-17’, the surface sediment analytical dataset; 3) ‘SBSP.SW_2010-18’, the primary surface water analytical dataset; 4) ‘SBSP.SW_Diel_2012-13’, the surface water diel sampling dataset; 5) ‘SBSP.QA_2010-18’, quality assurance data summary for the sediment and water datasets.

This dataset includes mercury and other constituent concentration and physical properties data for surface sediment, pore water and surface water collected as part of the South San Francisco Bay Salt Pond Restoration Phase 1 (2010 to 2018) studies. The overarching focus of these studies was to monitor mercury (Hg) biogeochemistry in both sediment and water in response to management actions associated with the conversion of former salt producing ponds to contemporary wetland habitat. The two primary management actions included the breaching of Pond A6 during December 2010, and the construction and operation of an adjustable tidal control structure (TCS) associated with the Pond A5/A7/A8 Complex beginning in June 2011. The TSC that reconnects the Complex to Alviso Slough (specifically referred to as the A8-TCS), a historically Hg contaminated waterway that represents the terminus of watershed drainage that includes the New Almaden mercury mining district. The A8-TCS consists of eight gates, each five feet wide. During the initial testing period (starting in June 2011) only one gate was opened, and the structure was closed again during the winter-spring months (from December until the following June). Over the subsequent seven years, the number of gates open was increased to three (15 feet, June 2012), to five (25 feet, September 2014), and eventually to all eight (40 feet, June 2017). Beginning in 2014 the A8-TCS was opened year-round. Field sampling occurred in both ponds and sloughs. In addition to sampling within the Complex ponds, two control ponds (A3N and A16) were also sampled. Similarly, in addition to sampling within Alviso Slough, two nearby control sloughs (Mallard Slough a.k.a Artesian Slough and Guadalupe Slough) were sampled (beginning in 2014 for Guadalupe Slough). Sediment sampling was conducted for the period of May 2010 through August 2011, which represents the period immediately prior to and immediately after the two above mentioned management actions. Additional sediment sampling was conducted in Mallard Slough exclusively during the August- September period 2011-2013, 2015, and 2017. Surface water sampling was conducted during three periods. The first period was in conjunction with the sediment sampling (May 2010 through August 2011). The second period involved a unique series of high temporal resolution sampling events conducted at a single site in mid-Alviso Slough, when water samples were collected hourly over a 25-hour period to capture the Hg dynamics associated with two full tidal cycles. A total of five such high-resolution ‘diel’ sampling events were conducted between May 2012 and February 2013, which included each of the four seasons and the annual ‘first flush’ event associated with the initiation of the 2012-13 rainy season. The third period, from February 2014 through February 2018, represents when all ponds and sloughs were again sampled (akin to the first period). This third period also represents when the A8-TCS was sequentially opened from 15 feet (3 gates open) to 40 feet (all 8 gates open), and when the A8-TCS management transitioned from being closed during the winter months to being opened year-round, beginning in 2014. This data release includes five data tables given both as Excel (*.xlxs) and machine readable 'comma-separated values' format (*.csv): 1) ‘SBSP.Data.Dictionary_2010-18’, the Data Dictionary, which provides definitions and details related to the other four data tables and includes analytical methods citations; 2) ‘SBSP.SED_2010-17’, the surface sediment analytical dataset; 3) ‘SBSP.SW_2010-18’, the primary surface water analytical dataset; 4) ‘SBSP.SW_Diel_2012-13’, the surface water diel sampling dataset; 5) ‘SBSP.QA_2010-18’, quality assurance data summary for the sediment and water datasets.

Comma-separated values (.csv) file containing data related to mercury in biota collected from Clear Lake California.

Comma-separated values (.csv) file containing data related to mercury in biota collected from Clear Lake California.

Methylmercury (MeHg) is a globally pervasive contaminant that biomagnifies in food webs and can reach toxic concentrations in consumers at higher trophic levels, including wildlife and humans. The production of MeHg, and its subsequent entry and biomagnification in food webs, is governed by a complex suite of biogeochemical, physical, and ecological processes, resulting in spatial variation in the distribution of MeHg. To better understand the link between MeHg production in sediments and MeHg bioaccumulation in biota, we evaluated the effects of habitat biogeochemistry, food web structure, and diet composition on bioaccumulation in the wetland-obligate California black rail (Laterallus jamaicensis coturniculus) at three wetlands along the Petaluma River in northern San Francisco Bay, California, USA. We also characterized meso-scale spatial variation by assessing differences among marsh subhabitats in sediment biogeochemistry and MeHg concentrations of sediments, surface waters, and tissues of biota.

Methylmercury (MeHg) is a globally pervasive contaminant that biomagnifies in food webs and can reach toxic concentrations in consumers at higher trophic levels, including wildlife and humans. The production of MeHg, and its subsequent entry and biomagnification in food webs, is governed by a complex suite of biogeochemical, physical, and ecological processes, resulting in spatial variation in the distribution of MeHg. To better understand the link between MeHg production in sediments and MeHg bioaccumulation in biota, we evaluated the effects of habitat biogeochemistry, food web structure, and diet composition on bioaccumulation in the wetland-obligate California black rail (Laterallus jamaicensis coturniculus) at three wetlands along the Petaluma River in northern San Francisco Bay, California, USA. We also characterized meso-scale spatial variation by assessing differences among marsh subhabitats in sediment biogeochemistry and MeHg concentrations of sediments, surface waters, and tissues of biota.

This dataset includes field measurements and laboratory analyses of surface water, bottom water (sediment-water interface), surficial (0-2 cm) sediment, pore water (0-2 cm), and biota collected in Lake Combie, California, from September 2017 through August 2021. The study area includes six sites within the reservoir where discrete samples of surface water, bottom water, sediment, and pore water were taken along the length of the reservoir at the following distances from the spillway: 0.07 miles, 0.5 miles, 0.9 miles, 1.2 miles, 1.3 miles, and 1.4 miles. The within-reservoir sites were sampled during September 2017, February 2018, and May 2018, prior to a large sediment removal operation, and again during September 2019, February 2020, and June 2020 following the removal operation. Zooplankton samples were collected at four of the six sites during the sampling period. Fish were collected from within two regions of the lake: in the Wooley Creek arm of the lower reservoir, and in the upper reservoir near the targeted area for sediment removal operations. Vertical profiles of water quality were measured with a multi-parameter sonde during water collection events and during one zooplankton event. Thirty-six surface water and thirty-six bottom water samples were collected at each site and analyzed for total mercury (filtered and particulate), methylmercury (filtered and particulate), total suspended solids, sulfate, chloride, selected dissolved nutrients, particulate 13-C/12-C and 15-N/14-N isotopic ratios, total particulate carbon and nitrogen, particulate carbon to nitrogen molar ratio, dissolved organic carbon, and dissolved organic-matter properties (absorption and fluorescence). Thirty-six bed-sediment samples were analyzed for total mercury, methylmercury, total reduced sulfur, and organic content. Pore water extracted from bed sediment was analyzed for filtered total mercury, filtered methylmercury, sulfate, chloride, selected dissolved nutrients, and dissolved organic carbon. Surface water, bottom water, and sediment collections included an additional four field replicates each for analysis - pore water had six replicates. One hundred six zooplankton samples and twenty-three replicates were analyzed for total mercury, methylmercury, 13-C/12-C isotopic ratio, and 15-N/14-N isotopic ratio. Two hundred ninety fish samples were analyzed for total mercury, methylmercury, 13-C/12-C isotopic ratio, 15-N/14-N isotopic ratio, and total mass carbon and nitrogen. Water-quality field measurements made with a multi-parameter sonde included water temperature, barometric pressure, specific conductance, dissolved oxygen, pH, and turbidity. The within-reservoir data includes seven data tables given as both machine readable tab-delimited text (*.txt) and Excel formats (*.xlsx): 1) DataDictionary_LCR17-21, the data dictionary, which provides definitions and details related to the six other data tables, and includes citations of analytical methods; 2) SurfWater_Field-Lab_LCR17-20, the surface water and bottom water data table; 3) Sediment_LCR17-20; 4) PoreWater_LCR17-20; 5) Zooplankton_LCR17-20; 6) Fish_LCR18-21; and 7) SurfWater_Profiles_LCR17-20.

This dataset includes field measurements and laboratory analyses of surface water, bottom water (sediment-water interface), surficial (0-2 cm) sediment, pore water (0-2 cm), and biota collected in Lake Combie, California, from September 2017 through August 2021. The study area includes six sites within the reservoir where discrete samples of surface water, bottom water, sediment, and pore water were taken along the length of the reservoir at the following distances from the spillway: 0.07 miles, 0.5 miles, 0.9 miles, 1.2 miles, 1.3 miles, and 1.4 miles. The within-reservoir sites were sampled during September 2017, February 2018, and May 2018, prior to a large sediment removal operation, and again during September 2019, February 2020, and June 2020 following the removal operation. Zooplankton samples were collected at four of the six sites during the sampling period. Fish were collected from within two regions of the lake: in the Wooley Creek arm of the lower reservoir, and in the upper reservoir near the targeted area for sediment removal operations. Vertical profiles of water quality were measured with a multi-parameter sonde during water collection events and during one zooplankton event. Thirty-six surface water and thirty-six bottom water samples were collected at each site and analyzed for total mercury (filtered and particulate), methylmercury (filtered and particulate), total suspended solids, sulfate, chloride, selected dissolved nutrients, particulate 13-C/12-C and 15-N/14-N isotopic ratios, total particulate carbon and nitrogen, particulate carbon to nitrogen molar ratio, dissolved organic carbon, and dissolved organic-matter properties (absorption and fluorescence). Thirty-six bed-sediment samples were analyzed for total mercury, methylmercury, total reduced sulfur, and organic content. Pore water extracted from bed sediment was analyzed for filtered total mercury, filtered methylmercury, sulfate, chloride, selected dissolved nutrients, and dissolved organic carbon. Surface water, bottom water, and sediment collections included an additional four field replicates each for analysis - pore water had six replicates. One hundred six zooplankton samples and twenty-three replicates were analyzed for total mercury, methylmercury, 13-C/12-C isotopic ratio, and 15-N/14-N isotopic ratio. Two hundred ninety fish samples were analyzed for total mercury, methylmercury, 13-C/12-C isotopic ratio, 15-N/14-N isotopic ratio, and total mass carbon and nitrogen. Water-quality field measurements made with a multi-parameter sonde included water temperature, barometric pressure, specific conductance, dissolved oxygen, pH, and turbidity. The within-reservoir data includes seven data tables given as both machine readable tab-delimited text (*.txt) and Excel formats (*.xlsx): 1) DataDictionary_LCR17-21, the data dictionary, which provides definitions and details related to the six other data tables, and includes citations of analytical methods; 2) SurfWater_Field-Lab_LCR17-20, the surface water and bottom water data table; 3) Sediment_LCR17-20; 4) PoreWater_LCR17-20; 5) Zooplankton_LCR17-20; 6) Fish_LCR18-21; and 7) SurfWater_Profiles_LCR17-20.

The Hamilton Wetland Restoration Project (HWRP) is a joint venture between the US Army Corps of Engineers (USACE; San Francisco District) and the California State Coastal Conservancy. The site is located on the property of the former Hamilton Army Airfield in Novato, California, along the western edge of San Pablo Bay, which is part of northern San Francisco Bay. The initial stages of wetland restoration, which included dredged sediment reuse, took place during 2009–2011. From 2011 until April 2014, the site was maintained as partially flooded through a temporary one-way culvert that allowed bay water onto the site. On April 25th, 2014, the outboard levee towards the north-eastern corner of the site was breached to restore tidal connectivity from the bay to the restoration area. The anticipated period for complete site restoration and marsh evolution is 10–15 years. During this period an active wetland vegetation replanting program was established by the USACE to augment the natural seeding by native plants. The various habitats on the restoration site include open-water sub-tidal, mudflats, emergent marsh, grassland, and upland transition zone. San Francisco Bay is contaminated with legacy mercury (Hg) from historic use in mining areas throughout the watershed, as well as from contemporary atmospheric and point-source inputs. Since wetlands are known to be particularly effective zones for the production of toxic methylmercury (MeHg) from inorganic Hg(II), the National Environmental Policy Act (NEPA) and California Environmental Quality Act (CEQA) documentation associated with the HWRP restoration identified MeHg production as a potentially significant impact of restoring the site to wetland habitat. As part of the USACE Monitoring and Adaptive Management plan (MAMP) for the restoration, the USACE was directed by the Regional Water Quality Control Board (RWQCB) and the San Francisco Bay Conservation and Development Commission (BCDC) to assess MeHg concentrations at the HWRP site. To fulfill this requirement, the USACE entered into an agreement with the U.S. Geological Survey (USGS) to conduct a multi-year and multi-phase investigation of mercury in biota (fish), water, and sediment at the HWRP site. The Sample and Analysis Plan (SAP) covers a period of 13 years and is divided into three phases. Phase 1 included the monitoring of sediment and water pre-breach [2013] and post-breach [2014], and the monitoring of fish pre-breach [2013 only]. Phase 2 covers the three-year period 2014-2016 (near-term post-breach). Phase 3 covers the nine-year period from 2017-2025 (long-term post-breach). Field sampling occurred once per year during a two-week window from mid to late June. A reference site, (Sonoma Baylands) managed by the U.S. Fish and Wildlife Service, was similarly sampled coincident with the HWRP site throughout the study. During the first year of study (2013, pre-breach), an additional reference site was sampled (China Camp), but was subsequently dropped. This data release summarizes the result to date for surface water and bed sediment. Fish data are not included. The list of surface water constituents include: filter-passing total mercury (THg) and methylmercury (MeHg); particulate THg, MeHg and divalent reactive mercury (RHg, operationally defined); particulate organic carbon (POC) along with the carbon-13 isotopic composition (δ 13C-POC); particulate nitrogen (PN) along with the nitrogen-15 isotopic composition (δ 15N-PN); total suspended solids (TSS); chlorophyll_a (Chl_a); specific conductance (SpC); dissolved oxygen (DO); pH; oxidation reduction potential (Eh); and temperature. The list of bed sediment constituents include: THg, MeHg, RHg, iron speciation [ferrous iron (Fe2+), crystalline and amorphous ferric iron (Fe3+)]; total reduced sulfur (TRS); Eh; organic content as percent loss on ignition (%LOI); grain size; porosity; bulk density; and temperature. This data release includes four data tables given both as Excel