The high economic and ecological value of estuaries is threatened by climate change, which is altering estuaries through changes in conditions on land, in the ocean, and in the atmosphere. As part of the Department of Energy’s Integrated Coastal Modeling Project, we are developing a 3-D physical–biogeochemical model of Delaware Bay, a large, coastal-plain estuary in the Mid-Atlantic region of the United States. The main purpose of the model will be to forecast changes in this estuary over the 21^st century. The model, which is based on the Regional Ocean Modeling System (ROMS), has 20 vertical levels in terrain-following coordinates and a horizontal resolution that varies from about 300 m in the tidal river to about 600 m in the lower bay. The biogeochemical component of the model is derived from the Estuarine Carbon and Biogeochemical model for the Chesapeake Bay (ChesROMS) and simulates numerous inorganic and organic nitrogen and carbon pools, as well as oxygen and alkalinity. A simulation is presented for 2007–2014 and evaluated with monthly surface measurements made by the Delaware River Basin Commission from April to October at 22 stations along the main axis of the estuary. The model is shown to be very skillful in simulating temperature and salinity, with coefficients of determination (R²) of 0.95 and 0.81, respectively. The model is considerably less skillful in simulating oxygen (R² = 0.44) and nitrate (R² = 0.22), with a large positive bias in the former (26 mmol m^–3) and large negative bias in the latter (27 mmol m^–3). The biogeochemical results suggest that net ecosystem production (photosynthesis minus respiration) is too high in the model. Photosynthesis in Delaware Bay is strongly light-limited, particularly in the upper portion of the estuary, and further analysis will investigate the model’s ability to simulate water clarity. The model is also missing wastewater inputs, which may be another reason why nitrate values in the model are too low. Once the model inputs are made more realistic and model parameters are suitably calibrated, the model will be applied to climate change scenarios using output from Department of Energy climate models, which will provide the appropriate boundary conditions at the estuary’s interfaces with land, ocean, and atmosphere.