While many studies have examined mesozooplankton feeding in coastal environments, less attention has been given to this subject in estuaries. We used bottle incubation experiments to measure the feeding rates of a cladoceran (Daphnia sp.), a calanoid copepod (Acartia spp.), and 2 cyclopoid copepods (Oithona davisae and Limnoithona tetraspina) on the protist plankton (<200 μm) of Suisun Bay, which is located in the upper San Francisco Estuary (SFE). Nanoplankton (2 to 15 μm) prey were highly abundant (2000 to 6000 cells ml-1 and 50 to 600 μg C l-1), whereas microplankton (15 to 200 μm) prey were 1 to 2 orders less abundant (10 to 90 cells ml -1 and 1 to 4 μg C l-1). There were few indications that mesozooplankton fed on nanoplankton, while microplankton were often significantly consumed. Daphnia sp. cleared all microplankton prey categories except diatoms at >2 ml predator (pred.)-1 h-1. O. davisae consumed only ciliates in September 2004, while in November 2004 it cleared both ciliates and diatoms at similar rates (0.8 ml pred.-1 h-1). L. tetraspina cleared only aloricate ciliates and flagellates (0.8 to 1.0 ml pred.-1 h-1). Acartia spp. had the highest clearance rates on diatoms of all the predators examined (mean <1.0 ml pred.-1 h-1) but cleared ciliates at even higher rates (>2.0 ml pred.-1 h-1). With respect to biomass ingestion, in every experiment mesozooplankton were found to ingest ciliate carbon at the highest rates (3 to 29 ng C pred.-1 h-1). Our results indicate that while estuarine mesozooplankton are often omnivorous, important species-specific differences exist, and microzooplankton, especially ciliates, are an important component of the upper SFE food web.