Comprehensive Mercury Studies

Science Center Objects

The objective specific to work conducted by the CAWSC is to produce a continuous time-series of suspended-sediment flux at an existing site in Alviso Slough.

Map datum and projection: NAD 83, UTM Zone 10
Map data: San Francisco Estuary Institute (habitats [adapted], pond boundaries, bay shoreline, aqueduct); Moffatt-Nichol Engineers (stormwater facilities); US Army Corps of Engineers (100-yr tide line); US Geological Survey (aerial photography); GreenInfo Network (upland open space [adapted], ownership [adapted]); EDAW, Association of Bay Area Governments, and Bay Area Open Space Council (trails [adapted]).
Map by: Michael May, Micha Salomon, and Gregory Tseng, San Francisco Estuary Institute.
Map date: May 30, 2006. Edited June 28, 2011.

The South Bay Salt Pond Restoration Project (SBSP Restoration Project) is one of the country's largest wetland restoration projects and plans to eventually restore approximately 15,000 acres of former salt evaporation ponds back to wetlands in South San Francisco Bay. This opportunity is unfortunately located in a mercury-rich environment due to historic and continuing runoff from the New Almaden Quicksilver Mine (the Guadalupe River watershed drains into the project area: Alviso Slough and adjacent ponds). One of the project's key scientific uncertainties is how tidal restoration could remobilize mercury-laden sediments or create environmental conditions that increase mercury methylation and bioaccumulation. In order to continue to restore tidal wetlands, the SBSP Restoration Project must monitor the changes in mercury's distribution, availability, and bioaccumulation that could be caused by project actions. Without this information, the SBSP Restoration Project will not be able to design restoration actions that avoid mercury mobilization and bioaccumulation, or, possibly, not even be allowed to implement future phases because of lingering concerns about mercury.

Two recent actions reconnecting salt ponds back to the Bay are of the most pressing concern. Pond A8 (and the hydrologically-connected Ponds A5 and A7) was opened to Alviso Slough in June 2011 through a water control structure, and Pond A6 was fully connected to tidal action through intentional levee breaches in December 2010. The objectives for the Comprehensive Mercury Studies Project are to answer key questions about these restoration actions:

  • Understand how much total mercury is mobilized due to scour of Alviso Slough from opening ponds to the tides.
  • Determine where the mercury moves (bay, ponds, or mudflats and neighboring marshes).
  • Investigate what effect the increased tidal action has on mercury methylation and bioaccumulation in fish and wildlife.
  • Examine the significance of these findings in a regional context.

The objective specific to work conducted by the CAWSC is to produce a continuous time-series of suspended-sediment flux at an existing site in Alviso Slough.

The Comprehensive Mercury Studies consist of six studies conducted by various USGS researchers. The work conducted by Shellenbarger and the CAWSC is for Study 2: Sediment Flux. This study will determine the net directional sediment flux in a tidal reach of Alviso Slough in between the two ponds opened to tidal action. Knowing the sediment flux is important because a large portion of the mercury is bound to and moves with sediment. We will utilize a continuously monitoring sediment flux station in Alviso Slough with a water-quality sonde to measure conductivity, temperature, pressure, and turbidity and an acoustic Doppler current profiler to measure velocity.

This project is aligned with several elements of the USGS Science Strategy: 1) The Role of Environment and Wildlife in Human Health by studying mercury in an area with significant recreation; 2) Energy and Minerals of America's Future because the source of mercury is from an upstream historic mercury mine; and 3) Understanding Ecosystems and Predicting Ecosystem Change by understand how perturbing the ecosystem for restoration may affect geomorphology of the habitat and sediment-mobilized mercury concentrations in biosentinels, such as fish.

Project Add-On: Comprehensive Mercury Studies In Alviso Slough, South San Francisco Bay (Project 2015-15)

study area at the southern end of San Francisco Bay

Map of the study area at the southern end of San Francisco Bay marking the locations of the deployment locations. Alviso Slough is the downstream reach of the Guadalupe River. The pond A5, A7, A8 complex is managed as a muted tidal pond, with water exchange at the A8 notch location and discharge from A7 into Alviso Slough.

(Public domain.)

Map of the study area at the southern end of San Francisco Bay marking the locations of the deployment locations. Alviso Slough is the downstream reach of the Guadalupe River. The pond A5, A7, A8 complex is managed as a muted tidal pond, with water exchange at the A8 notch location and discharge from A7 into Alviso Slough.

We have been collecting suspended-sediment flux data in Alviso Slough since WY2011. This involved deploying a water quality sonde (CTD-DO, turbidity) and an upward looking acoustic Doppler current profiler (ADCP) in the thalweg of the slough. Regular site visits went from initially every six weeks to every three weeks in 2014, because of the loss of data due to instrument fouling (particularly from fine sediments packing in the conductivity cell). Periodic boat-based discharge measurements and EDIs were collected to calibrate the index velocity station to the cross sectional slough conditions. In May 2014, we installed a near-surface CTD to help better understand the vertical gradients in the slough that can affect material transport.

The largest current data gap is knowledge of the horizontal gradients of temperature, salinity, and suspended sediment. Alviso Slough is a highly variable system, where freshwater enters from the Guadalupe River and Bay-salinity water is at the mouth at the confluence with Coyote Creek. The slough also experiences tides that exceed three meters and can drive water up-slough more than four kilometers, which creates strong gradients in density that can have a dramatic effect on transport processes in the Slough. Additionally, water enters and exits the slough though a gate in pond A7, the notch in pond A8, and the breaches in A6. Water that spends time in the ponds may be discharged back to the slough having different chemical characteristics, further complicating the dynamics of this system. This proposed new work includes the collection of horizontal gradient data in Alviso Slough that are required for proper hydrodynamic and sediment transport model calibration. We will install a water quality sonde at the confluence of Alviso Slough and Coyote Creek to capture data at the bay-side boundary. Additionally, we will install a water quality sonde and current meter outside of the managed pond A8 notch to help understand the upstream gradients and the direction of net sediment flux for pond A8. The information from these stations will be used to augment the data we are collecting in mid-Alviso Slough.

Water quality and sediment supply and transport are critical information for the South Bay Salt Pond Restoration Project, the South San Francisco Bay Shoreline Study, transport of sediment-associate contaminants, and the calibration and validation of transport models. In addition to our original objective of quantifying the mass flux of suspended sediment in Alviso Slough, we have two new objectives:

  1. Quantify suspended-sediment flux in and out of managed pond A8 (upstream of our original station) and compare this flux to that measured at the original station.
  2. Deploy a water quality sonde (CTD-DO, turbidity) at the mouth of Alviso Slough to understand far-field sediment concentrations at the junction with Coyote Creek and provide data for calibration and validation of a suspended-sediment transport model being developed for Alviso Slough.