Shallow-water habitats are being restored in the Sacramento-San Joaquin River Delta with the goal of enhancing phytoplankton production and food availability for higher trophic levels. However, elevated grazing pressure from the non-native freshwater clam Corbicula fluminea and localized depletions of dissolved inorganic nitrogen may limit phytoplankton biomass accumulation in restored habitats. To evaluate interactions between nutrients and grazing on phytoplankton productivity and biomass accumulation, Sacramento River water high or low in phytoplankton biomass was amended with wastewater effluent, presence of C. fluminea, or both, in 48 h in situ incubations. We measured changes in chl a concentration, phytoplankton community composition, and photosynthetic efficiency as well as carbon and nitrogen uptake rates as indicators of phytoplankton responses. Diatoms dominated phytoplankton communities before and after incubation. Chl a concentrations increased 0.7 and 7.4 times in the high and low phytoplankton biomass controls, respectively, and 4.5 and 14 times in the high and low phytoplankton biomass effluent-added treatments, respectively. In the clam treatments, chl a accumulation was suppressed to near zero regardless of effluent additions or initial phytoplankton biomass. In treatments with clams and effluent combined, phytoplankton photosynthetic efficiency was nearly 50% lower than in the effluent-only treatments, suggesting phytoplankton were stressed in the presence of clams. This experiment demonstrated that the presence of clams can prevent the accumulation of phytoplankton biomass, both directly by clam filtering and indirectly by depressing phytoplankton photosynthetic efficiency and rate of growth. We recommend that future wetland restoration projects promoting increased phytoplankton biomass assess clam settlement likelihood as well as nutrient availability.