The eastern oyster, Crassostrea virginica, is a filter feeding organism that can strongly affect the environment in which it lives, including removal of suspended particulate matter from the water column and enhancement of benthic fluxes of carbon, nitrogen and phosphorus. As a result, oyster reefs can make a substantial contribution to total benthic oxygen uptake. Within the Virginia Coast Reserve (VCR), The Nature Conservancy (TNC), in partnership with state and federal agencies, are conducting large-scale efforts to restore C. virginica reefs. Due to their complex ecosystem structure, quantifying restoration success has proven difficult. In combination with population measurements, we are quantifying the benthic oxygen flux to determine net ecosystem respiration in order to quantify how closely restoration reefs are functioning like native reefs. Aquatic eddy covariance measurements of oxygen fluxes were made over several reefs of varying health and over an adjacent mud flat. Preliminary data suggest that oxygen uptake is approximately 10 times higher for a healthy oyster reef compared to an adjacent mud flat, suggesting that oyster reefs have the potential to sequester large amounts of carbon as they grow and develop. As more data become available, we will be able to further quantify the functioning of oyster reefs as well as the success of restoration efforts within the VCR.