Benthic invertebrate communities are monitored because the composition of those communities can affect 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 acute and chronic stressors in an environment because they accumulate contaminants and can respond – sometimes dramatically - to oligotrophic and eutrophic conditions. Benthic communities affect water quality by grazing pelagic food resources and increasing the rate of nutrient regeneration through feeding and bioturbating sediments. 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 owing to poor light conditions caused by high turbidities, and high grazing losses from the water column by benthic invertebrates and zooplankton. However, the balance of biogeochemical conditions in most springs accommodates a short phytoplankton bloom in South San Francisco Bay. This balance between available light, nutrients, and grazing has maintained the phytoplankton biomass in South San Francisco Bay at low levels relative to other high-nutrient urban estuaries. The role of benthic invertebrates during these episodic spring events, as well as in other seasons, remains of great interest to water-quality and biological resource managers.