Quantitative measurements of phytoplankton removal in a natural setting are needed to evaluate interactions between aquacultured bivalve populations and the surrounding environment. We report high-frequency (15-min) measurements of environmental variables relevant to oyster feeding and excretion at the inflow and outflow of an oyster nursery—floating upweller system (FLUPSY)—from June through September 2010 in the East Creek embayment, Peconic Estuary, NY. We demonstrated large variability in oyster particle clearance rate on short- (minutes to hours) to long-term (seasonal) timescales, including oyster responses to environmental variation, such as diurnal temperature and dissolved oxygen cycles, wind-driven turbulence, and the presence of harmful algae. A diel cycle in clearance rates calculated from whole FLUPSY measurements was apparent, with a maximum weight-specific clearance rate (CR_W) of 2.21 L/h/g occurring around midnight, and a minimum CR_W of 0.32 L/h/g at 0740 HR, coincident with the lowest concentration of dissolved oxygen in the water. Throughout the season, oyster growth and feeding showed constant, high values from June 12 to July 21, with a median CR_W of 0.95 L/h/g. From late July to September, a toxic dinoflagellate, Cochlodinium polykrikoides, was present frequently in the water, and was coincident with depressed oyster feeding, slow/no growth, and increased mortality. Overall, the FLUPSY in East Creek did not have a large impact on the abundance of phytoplankton in the water. Future modeling efforts projecting carrying capacity and ecosystem services of shellfish aquaculture and restoration need to take into account the potential for temporal variability in feeding resulting from environmental variation, as observed in this study.