Estuaries and coastal marine ecosystems receive large inputs of nutrients, organic carbon, and sediments from non—point—source runoff from terrestrial ecosystems. In the tidal, freshwater Hudson River estuary, such inputs are the major sources of organic carbon, driving ecosystem metabolism, and thus strongly influencing dissolved oxygen concentrations. We used a watershed simulation model (GWLF) to examine the controls on inputs of organic carbon and sediment to this estuary. The model provides estimates of water discharge, sediment inputs, and organic carbon inputs that agree reasonably well with independent estimates of these fluxes. Even though the watershed for the Hudson River estuary is dominated by forests, the model predicts that both sediment and organic carbon inputs come overwhelmingly from urban and suburban areas and from agricultural fields. Thus changes in land use within the Hudson River basin may be expected to altering inputs to the estuary, thereby altering its metabolism. Precipitation is important in controlling carbon fluxes to the estuary, and so climate change can be expected to alter estuarine metabolism. However, the day—to—day and seasonal patterns of precipitation appear more important than annual mean precipitation in controlling organic carbon fluxes.