ABSTRACT: Eastern oysters Crassostrea virginica and hard clams Mercenaria mercenaria are key organisms for both the ecosystem services they provide and for their commercial value, but their populations have declined greatly worldwide. In an attempt to understand the interaction between bivalve physiology and environmental conditions, filter-feeding assays were carried out in a shallow estuary, the Indian River Lagoon (IRL; Florida, USA). The feeding behavior of the bivalves was studied using in situ filter-feeding devices and the biodeposition method in the 3 basins of the IRL during March and August 2015. Water characteristics (temperature, salinity, dissolved oxygen, chl a, and total, organic, and inorganic particulates) were related to possible changes in the feeding physiology of the bivalves. Oysters had higher clearance rates, filtration rates, and rejection than clams. The high rejection of inorganic matter allowed oysters to increase the organic matter ingested, leading to high absorption efficiencies. In contrast, because clam rejection was low regardless of elevated levels of inorganic matter, their absorption efficiency only increased with higher organic matter content. Both species preferred higher salinities, and the amount of organic matter in the water had a negative relationship with some feeding parameters (filtration rate for both species, and rejection for oysters). Acute environmental change brought about by a brown tide (caused by the alga Aureoumbra lagunensis) also affected these 2 bivalve species differently, supporting the hypothesis that oysters and clams have different physiological capabilities that drive their ability to survive in dynamic estuarine ecosystems.