Abstract. Carbonate geochemistry research in large estuarine systems is limited and widely understudied. Further, changes in land use activity have profoundly influenced watershed export of organic and inorganic carbon, acids, and nutrients to the coastal ocean. To investigate the seasonal variation of the inorganic carbon system in the Delaware Estuary, one of the largest estuaries along the U.S. east coast, dissolved inorganic carbon (DIC), total alkalinity (TA), and pH were measured down the estuary from June 2013 to April 2015. In addition, to explore how drainage basin mineralogy, weathering intensity, and tributary discharge impact total riverine DIC and TA fluxes to the estuary and export fluxes to the ocean, DIC, TA, and pH were periodically measured from March to October 2015 in the non-tidal freshwater Delaware, Schuylkill, and Christina rivers. Strong negative relationships between river TA and discharge support that changes in HCO3− concentrations reflect the dilution of the weathering derived products in the drainage basin. The ratio of DIC to TA, a rarely studied but important property, is high (1.11) during high discharge and low (0.94) during low discharge, reflecting additional CO2 input most likely from land surface organic matter decomposition other than HCO3− input from the drainage basin weathering processes. Our data further suggest that DIC in the Schuylkill River can be substantially different from DIC in the Delaware River, and thus in any river system, tributary contributions must be considered when addressing DIC inputs to the estuary. Long-term records of increasing alkalinity in the Delaware and Schuylkill river support global shifts toward higher alkalinity in estuarine waters with time. Annual DIC input flux to the estuary and export flux to the ocean are estimated to be 15.7 ± 8.2 × 109 mol C yr−1 and 16.5 ± 10.6 × 109 mol C yr−1, respectively. CO2 flux produced within the estuary inclusive of inputs from intertidal marshes is small (5.1 × 109 mol C yr−1) when compared to total riverine flux. This finding suggests that, in the case of the Delaware Estuary and perhaps other large coastal systems with long freshwater residence times, the majority of the DIC produced by biological processes is exchanged with the atmosphere rather than exported to the sea. Based on a CO2 mass balance model, we concluded that annually the Delaware Estuary is a weak heterotrophic system (−1.3 ± 3.8 mol C m−2 yr−1), which is in contrast to many highly heterotrophic smaller estuaries.