Oyster restoration efforts and aquaculture have increased globally to counteract the overall decline of intertidal and subtidal oyster reefs to less than 15% of historical populations. Sustainability efforts to increase oysters in the Chesapeake Bay are of particular interest because oysters provide ecosystem services that may be applied as best management practices (BMPs) to reduce nitrogen inputs, which are the primary cause of eutrophication and its consequences. Although observations show that denitrification associated with oysters effectively removes nitrogen, methodologies vary widely, and mechanisms that control denitrification remain poorly understood. First, I determined the role of oysters relative to sediments on oyster reef biogeochemical fluxes. Next, I compared in situ and ex situ methods for the determination of biogeochemical fluxes associated with oysters. Finally, I conducted field sampling and experiments to characterize how on-bottom oyster aquaculture impacts nitrogen biogeochemistry. In situ approaches for measuring oyster denitrification and other biogeochemical fluxes are logistically challenging, but incubations must include oysters if the goal of the research is to accurately quantify oyster reef biogeochemical fluxes. Regression of oyster clump fluxes against the oyster tissue biomass indicates significant positive relationships for O2 and NH4+, marginally significant and positive relationships for dissolved inorganic carbon (DIC) and N2, and no significant relationship for NOx or soluble reactive phosphorus (SRP). Above a restored oyster reef, time series and ensemble-averaged normalized profiles from in situ methods reveal that oxygen was removed, whereas DIC, NH4+, N2, and SRP were produced at the sediment-water interface. Besides NOx, N2, and SRP, all in situ derived fluxes measured over the oyster reef were in the same direction as benthic chamber flux estimates. In addition, fluxes measured across an oyster aquaculture lease show that denitrification was stimulated at the harvested sites during sampling in May and September. Although harvested sites exhibited higher rates of denitrification, seasonal differences in rates were likely dependent on ambient NOx concentrations and availability of labile organic matter. Furthermore, seasonal shifts in oyster biomass for a given oyster length from the lease mirrored changes in average oyster-associated denitrification rates from May to September. Oyster biomass was associated with changes in denitrification rates, but the relationships changed depending on the sampling month. This work provided an opportunity to investigate whether sediment-based biogeochemical concepts hold true for oysters and learn about the influence of oysters and associated activities on overall biogeochemistry. Therefore, provided that oysters are grown in favorable denitrification environmental conditions, this work adds to the growing consensus that oysters can play an important role in mitigating nitrogen in coastal areas.