The Regional Ocean Modeling System (ROMS) has been coupled with the Water Quality Analysis Simulation Program (WASP) to be used in a comprehensive analysis of water quality in Barnegat Bay, New Jersey. The coupler can spatially aggregate hydrodynamic information in ROMS cells into larger WASP segments. It can also be used to resample ROMS output at a finer temporal scale to meet WASP time-stepping requirements. The coupler aggregates flow components, temperature, and salinity in ROMS output for input to WASP via a hydrodynamic linkage file. The coupler was tested initially with idealized cases designed to verify the water mass balance and conservation of constituent mass using one-to-one and one-to-many connectivity options between segments. A realistic example from the Toms River embayment, a subdomain of Barnegat Bay, was used to demonstrate the functionality of the coupling. A WASP eutrophication model accounting for dissolved oxygen (DO), nitrogen, and constant phytoplankton concentrations was applied to explore the distribution and trends in DO and nitrogen in the embayment for the period of July–August 2012. Results of DO modeling indicate satisfactory agreement with measurements collected at in-bay stations and also indicate that this coupled approach, despite substantial differences in spatiotemporal discretization between the models, provides adequate predictive capabilities.