Sediment Remobilization of Mercury in South San Francisco
Bay, California

By Brent R. Topping, James S. Kuwabara, Mark C. Marvin-DiPasquale, Jennifer L. Agee, Le H. Kieu, John R. Flanders, Francis Parchaso, Stephen W. Hager, Cary B. Lopez, and David P. Krabbenhoft



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September 2004


Scientific Investigations Report 2004-5196

U.S. Department of the Interior

U.S. Geological Survey


Field and laboratory studies were conducted in April and November 2003 to provide the first direct measurements of the benthic flux of dissolved mercury species (total and methylated forms) between the bottom sediment and water column at two sampling locations within the southern component of San Francisco Bay, California (hereafter referred to as South Bay): one within the main channel and the other in the western shoal area. Because of interest in the effects of historic mercury mining within watersheds that drain into South Bay, the solutes of primary interest were dissolved-mercury species and the predominant ligands that often control mercury speciation (dissolved sulfide and dissolved organic carbon). Benthic flux, sometimes referred to as internal recycling, is the transport of dissolved chemical species between the water column and the underlying sediment. Because of the affinity of mercury to adsorb onto particle surfaces and to form insoluble precipitates (particularly with sulfides), the mass transport of mercury in mining-affected watersheds is typically dominated by particles. As these enriched particles accumulate at depositional sites such as estuaries and reservoirs, benthic processes facilitate the repartitioning, transformation, and transport of mercury in dissolved, biologically reactive forms (dissolved methyl-mercury being the most bioavailable for trophic transfer). These are the forms of mercury examined in this study.


During two sampling events, three replicate sediment cores from each of two South Bay locations were used in incubation experiments to provide flux estimates and benthic biological characterizations. Incubation of these cores provided “snapshots” of solute flux across the sediment-water interface in this component of the estuary, under environmental conditions representative of the time and place of collection. Ancillary data, including nutrient and ligand fluxes, were gathered to provide a water-quality framework from which to compare the results for mercury. The following major observations from interdependent physical, biological, and chemical data were made:

Physical and Biological Characterizations

  1. Porosity: The surficial sediment at Station 29A was generally of higher porosity than that at Station 25 on both sampling dates. Station 29A porosities ranged from 0.77 to 0.92 (0.84 + 0.05), while those of Station 25 ranged from 0.73 to 0.82 (0.77 + 0.04). This difference, however, is not statistically significant at the 95% confidence interval.
  2. Benthic Biota: Macroinvertebrate densities varied temporally and spatially, in a manner consistent with previous studies (Topping and others, 2001; see macroinvertebrate discussion). Given that the first sampling event coincided with the annual spring phytoplankton bloom in the South Bay, Chlorophyll and phaeophytin concentrations also exhibited temporal and spatial differences. See the results section for details.

Chemical Characterizations

Note: The dissolved-mercury concentrations discussed in this section refer to samples filtered with 0.7-micrometer quartz-fiber filters pre-combusted at 500 oC for 12 hours.

  1. Dissolved mercury in the water column: Dissolved methyl-mercury concentrations were below detection limits at all sites and dates. Total dissolved-mercury concentrations ranged from ~4 to ~10 picomolar, so the undetectable methyl-mercury values were not surprising because total mercury concentrations are typically two or more orders of magnitude greater than methylmercury concentrations. Total dissolved-mercury concentrations were appreciably elevated at the western-shoal Station 25 relative to the main-channel Station 29A, and in spring relative to autumn.
  2. Benthic flux of dissolved forms of mercury: When the three cores for each site were averaged, benthic flux estimates for total dissolved-mercury showed no temporal change for Station 25, but showed higher flux in spring relative to fall for Station 29A. Still, the averages for each site and date were within the same order of magnitude. When the average for all sites and dates (135 ± 94 g/day; is extrapolated over the greater South Bay, the magnitude of the values is consistently comparable to or greater in magnitude than estimates of major riverine sources. Notably, benthic flux of dissolved mercury is of the same magnitude as particulate mercury inputs from the Guadalupe River watershed (318 ± 88 g/day in 2003; McKee 2004, draft copy). Transport of dissolved-mercury species between the estuary bed and water column may therefore be a potentially critical process regulating the fate of mercury species in the water column (Mercury flux discussion).

    All twelve individual core incubations in the study resulted in positive total-mercury flux values. In other words, at all sites and dates, each core indicated that dissolved total mercury was transported out of the sediment into the overlying water column.

    Dissolved methyl-mercury fluxes could not be directly calculated due to the undetectable values for all sites and dates (<0.5 picomolar in May, <0.2 picomolar in November). These undetectable values are common and have been observed in other studies (Conaway and others, 2003). However, when comparing loads of dissolved methyl-mercury into South Bay, benthic flux cannot be summarily discounted as a possible source due to analytical limitations (Load comparison discussion).

    Ancillary measurements characterizing the sediment were compared with water-column and benthic flux values. Four correlations were observed including sediment mercury’s correlation with benthic flux of dissolved mercury (Ancillary sediment characterization discussion).
  3. Benthic flux of mercury-binding ligands:

    Dissolved-sulfide benthic fluxes were similar at all dates and sites, and consistently positive. Sulfides are associated with reducing conditions, so the similarities at all stations and dates might indicate reducing-oxidizing (redox) conditions were similar throughout the study, despite significantly higher dissolved oxygen (DO) consumption in May (DO discussion). Given that the South Bay water column is consistently oxic (that is, dissolved-sulfide species are only metastable), the relative consistency of the mercury fluxes may be associated with the flux of sulfides, which have a strong affinity to complex with mercury. Dissolved organic carbon (DOC) fluxes were markedly different between sites and significantly so between dates. Autumn fluxes were much higher than spring fluxes at both sites, while Station 29A exhibited higher fluxes than Station 25 for both dates. Unlike sulfides, negative DOC fluxes (solute transport from the water column to the bottom sediment) were observed in some cores.
  4. Benthic flux of other metals:

    Comparisons between this study and a previous one by the authors (Topping and others, 2001) indicated that 2003 conditions may be less conducive to metal remobilization and release than in previous years (Dissolved nickel and copper discussion). This indicates that estimates of longterm mercury flux could be incorrectly low if based only on 2003 sampling.

Upgradient Remedial Implications


Because the benthic flux of mercury appears to represent a dominant transport process for dissolved, more bioavailable forms, an important management implication is suggested. Remediation efforts and Total Maximum Daily Load (TMDL) allocations along the Guadalupe River have dual objectives of decreasing concentrations and loads to down-gradient systems in an effort to reduce bioaccumulation of mercury in fish consumed by humans and wildlife. Using preliminary mercury-flux estimates into the estuary, our results indicate that a significant (and possibly predominant) percentage of dissolved mercury in the water column presently comes from the bay sediment (Mercury flux discussion). If upstream sources are controlled, which is desirable even apart from estuary effects, the change in inflow loads is likely to be compensated in part by increases in benthic flux.


Comment on the Report Structure


In contrast to typical scientific manuscripts, this report is formatted in a pyramid-like structure to serve the needs of diverse groups who may be interested in reviewing or acquiring information at various levels of technical detail. The report enables quick transitions between the initial summary information (figuratively at the top of the pyramid) and the later details of methods or results (figuratively towards the base of the pyramid) using hyperlinks to supporting figures and tables, and an electronically linked Table of Contents.


Executive Summary

Physical and Biological Characterizations

Chemical Characterizations

Remedial Implications


Results and Discussion

Physical Data

Biological Data

Chemical Data

Study Design and Methods

Coring Operation

Core Incubations

Physical Data

Biological Data

Chemical Parameters

References Cited


Appendix 1: Comments on the Report Structure

Appendix 2: List of Figures

Appendix 3: List of Tables


For additional information write to:


Brent R. Topping
U.S. Geological Survey
345 Middlefield Road, MS 439
Menlo Park, CA 94025


Copies of this report may be obtained from the authors or


U.S. Geological Survey
Information Center
Box 25286, MS 517
Denver Federal Center
Denver, CO 80225


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