Benthic response to water quality and biotic pressures in lower south San Francisco Bay, Alviso Slough, and Coyote Creek

Open-File Report 2015-1234
By: , and 



Benthic invertebrate communities are monitored because the composition of those communities can effect and be affected by the water quality of an aquatic system. Benthic communities use and sometimes regulate the cycling of essential elements (for example, carbon). Benthic invertebrate taxa may also indicate acutely and chronically stressful environments because they are mostly sessile, accumulate contaminants, and sometimes respond dramatically to oligotrophic as well as eutrophic conditions. Benthic communities can in turn affect water quality by grazing pelagic food resources and increasing the rate of nutrient regeneration through feeding and bioturbating the sediment. 

South San Francisco Bay is a system dependent on phytoplankton as the base to the food web. Despite abundant nutrients, south San Francisco Bay has had limited phytoplankton production in the last several decades owning to poor light conditions and high grazing losses from the water column by benthic invertebrates. The south San Francisco Bay achieves a balance of biogeochemical conditions in most springs to accommodate a short phytoplankton bloom. This balance has maintained the phytoplankton in south San Francisco Bay at low biomass levels relative to other high-nutrient urban estuaries. The role that benthic invertebrates play in this balance, in these episodic spring events, and in other seasons within the estuary remains of great interest to water-quality and biological resource managers. 

Our primary objective in this study is to quantify current (2014) benthic-community structure and function in the south San Francisco Bay sloughs and to compare those communities temporally over decadal time scales with a unique long-term dataset. The study area (fig. 1) is inclusive of the area south of the Dumbarton Bridge (DB) including Alviso and Guadalupe Sloughs and Coyote Creek. 

The following are results highlighted in this report: 

  • The benthic communities of Coyote Creek and Alviso, Guadalupe, and Artesian Sloughs were dominated by different organisms but similar functional groups in March, June, and September 2014. 
  • Coyote Creek stations (D3 and CC1) had a similar increase in Potamocorbula amurensis biomass followed by a decline in 2014, as was observed annually in the south San Francisco Bay since 1999. The lack of grazing pressure owing to the observed declines in these taxa in 2014 may allow the sloughs to become sources of phytoplankton in spring. 
  • Bivalve biomass is elevated in summer and fall relative to the spring and winter except in Artesian Slough, where bivalves did not establish a signifcant presence. Presence of certain species contributes to the prey value of the community to predators. Potamocorbula amurensis is a shallow-burrowing bivalve and hence is easy prey for bottom-feeding predators. In contrast, Macoma petalum is a deposit feeder and can burrow deeper into the substrate than Potamocorbula amurensis, making it harder to be preyed upon. The quantitative importance of such predator-prey relationships on phytoplankton dynamics requires further investigation. There were also more amphipods in the sloughs in March 2014; this group is another potential contributor to the benthic-pelagic biomass balance. There is no observed reason for Artesian Slough to have low bivalve biomass values and high amphipod abundances. 

Suggested Citation

Parchaso, F., Thompson, J.K., Crauder, J.S., Anduaga, R.I., and Pearson, S.A., 2015, Benthic response to water quality and biotic pressures in lower south San Francisco Bay, Alviso Slough, and Coyote Creek: U.S. Geological Survey Open-File Report 2015–1234, 44 p.,

ISSN: 2331-1258 (online)

Study Area

Table of Contents

  • Executive Summary
  • Introduction
  • Methods 
  • Results and Observations
  • Conclusions
  • References Cited 
  • Appendixes 1–18

Additional publication details

Publication type Report
Publication Subtype USGS Numbered Series
Title Benthic response to water quality and biotic pressures in lower south San Francisco Bay, Alviso Slough, and Coyote Creek
Series title Open-File Report
Series number 2015-1234
DOI 10.3133/ofr20151234
Year Published 2015
Language English
Publisher U.S. Geological Survey
Publisher location Reston, VA
Contributing office(s) National Research Program - Western Branch
Description iv, 44 p.
Country United States
State California
Other Geospatial Alviso Slough, Coyote Creek, San Francisco Bay
Online Only (Y/N) Y
Additional Online Files (Y/N) N
Google Analytic Metrics Metrics page
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