AbstractA small, turbid and nutrient-rich tributary, the Murderkill Estuary, and a large estuarine ecosystem, the Delaware Bay, are tightly linked and form an efficient, tidally-coupled biogeochemical reactor during the summer. Nitrate loading from the Murderkill Estuary generates an instantaneous increase in biological oxygen production in the adjacent Delaware Bay. We are able to capture this primary production response with continuous hourly measurements of dissolved oxygen, chlorophyll, and nitrate. The nitrate influxes from the Murderkill support primary production rates in the Delaware Bay margins that are twice as high as the average production rates measured in the central Bay regions. This elevates chlorophyll in the Bay margins in the summer and fuels metabolism. Tidal transport of the newly produced autochthonous chlorophyll particles from the Bay into the Estuary could also provide a source of labile material to the marshes surrounding the Murderkill, thus perhaps fueling marsh respiration. As a consequence of the tidal coupling between Delaware Bay and the Murderkill Estuary, ecosystem productivity and metabolism in the Bay and Estuary are linked, generating an ecosystem feedback mechanism. Storms modulate this tidally-coupled biogeochemical reactor, by generating significant nitrate and salinity changes. Depending on their magnitude and duration, storms induce large phytoplankton blooms in the Delaware Bay. Such large phytoplankton blooms may occur more often with climate change, since century-long discharge records document an increase in storm frequency.