Air-water CO2 fluxes in estuarine environments are characterized by high interannual variability, in part due to hydrological variability that alters estuarine carbonate chemistry through multiple physical and biogeochemical processes. To understand the relative contributions of these varied controls on interannual air-water CO2 fluxes in the mainstem Chesapeake Bay, we implemented both hindcast and scenario simulations using a coupled physical-biogeochemical model. Significant spatiotemporal variability in bay-wide fluxes was found over a 10-year period (1996-2005), where the mainstem Bay was primarily a net CO2 sink, except in drought periods. Sensitivity scenario results suggested substantial effects of riverine nutrient and organic matter (OM) inputs to CO2 flux variations. The high correlations between riverine inputs and upper-Bay fluxes were due to elevated respiration under increased OM inputs. The interannual flux variations in the lower Bay was mostly regulated by the nutrient inputs. Both nutrient and OM inputs contributed to the flux variability in the mid Bay. It is found that the interannual CO2 flux of the mainstem was most sensitive to riverine nutrient inputs associated with the hydrological changes. For each hindcast simulation we computed the ratio of organic carbon turnover time to water residence time (λ), a proxy for CO2 efflux potential, and found that the wetter periods had a relatively lower λ. The variability of mainstem CO2 fluxes can be well represented using a generic function of λ. The model results showed that higher river flows would lead to enhanced CO2 sinks into a large eutrophic estuary by promoting net autotrophy.