Human activities have resulted in an array of stressors to coastal ecosystems. In the context of ecosystem function, two prominent changes have been nutrient enrichment and precipitous declines in the population of the eastern oyster, Crassostrea virginica. Although historically valued as a fishery, oysters provide broader ecological functions, which include filtering water thereby reducing turbidity as they feed and providing habitat for fish and crabs. Despite decades of oyster research, we lack a comprehensive understanding of how oysters influence nitrogen biogeochemistry in estuarine ecosystems. My research directly assessed the role of oysters in enhancing sediment denitrification and the efficacy of oyster reef restoration in alleviating nutrient pollution. I measured net N2 fluxes from five major estuarine habitats: salt marshes, seagrass beds, oyster reefs and intertidal and subtidal flats. Given the current habitat distribution in this study system, denitrification (N2 production) removed approximately 76% of the estimated watershed nitrogen load. Microcosm experiments were conducted to examine the direct effects of individual oysters on nitrogen dynamics. Results indicated that biodeposit production and excretion shifted sediments from a nitrogen source to a nitrogen sink. Experimental plots of live oysters, oyster shells and mud flats were used to distinguish between the effects of oyster feeding and reef structure on sediment denitrification. The production and accumulation of biotic material accounted for 60% of denitrification from oyster reef sediments while 40% was attributed to the abiotic effects of the reef structure. Fluxes measured from restored intertidal oyster reef sediments demonstrated that oyster reefs prime sediments for enhanced denitrification in response to anthropogenic nitrogen loading; however, the magnitude of this effect is dependent on the habitat setting of the oyster reef. This research identified mechanisms by which oysters alter sediment nitrogen dynamics and enhanced our understanding of oyster reef impacts on ecosystem function. This information is critical for determining where to focus reef restoration and preservation efforts to produce the greatest benefit. Results from my research will inform management strategies, restoration projects and policies aimed at improving water quality and sustaining healthy estuarine ecosystems.