Prior studies of the phytoplankton dynamics in South San Francisco Bay, California, USA have hypothesized that bivalve filter-feeders are responsible for the limited phytoplankton blooms in the system. This study was designed to examine the effects of benthic grazing and light attenuation on this shallow, turbid, and nutrient replete system. We found that grazing by shallow water bivalves was important in determining phytoplankton bloom occurrence throughout the system and that above a shallow water bivalve grazing threshold, phytoplankton biomass did not exceed bloom levels. Wind speed, used as a proxy for light attenuation in the shallow water, was similarly important in determining bloom development in the shallow water. Environmental conditions and benthic grazing in the deep water channel had a less discernible effect on system-wide phytoplankton blooms although persistent water column stratification did increase bloom magnitude. The shallow water bivalves, believed to be preyed upon by birds and fish that migrate through the system in fall and winter, disappear each year prior to the spring phytoplankton bloom. Because growth of the phytoplankton depends so strongly on shallow water processes, any change in the shallow-water benthic filter-feeders or their predators has great potential to change the phytoplankton bloom dynamics in this system. ?? 2007 Elsevier B.V. All rights reserved.