Variable density ground water flow models are rarely used to estimate submarine ground water discharge because of limitations in computer speed, data availability, and availability of a simulation tool that can minimize numerical dispersion. This paper presents an application of the SEAWAT code, which is a combined version of MODFLOW and MT3D, to estimate rates of submarine ground water discharge to a coastal marine estuary. Discharge rates were estimated for Biscayne Bay, Florida, for the period from January 1989 to September 1998 using a three-dimensional, variable density ground water flow and transport model. Hydrologic stresses in the 10-layer model include recharge, evapotranspiration, ground water withdrawals from municipal wellfields, interactions with surface water (canals in urban areas and wetlands in the Everglades), boundary fluxes, and submarine ground water discharge to Biscayne Bay. The model was calibrated by matching ground water levels in monitoring wells, baseflow to canals, and the position of the 1995 salt water intrusion line. Results suggest that fresh submarine ground water discharge to Biscayne Bay may have exceeded surface water discharge during the 1989, 1990, and 1991 dry seasons, but the average discharge for the entire simulation period was only ???10% of the surface water discharge to the bay. Results from the model also suggest that tidal canals intercept fresh ground water that might otherwise have discharged directly to Biscayne Bay. This application demonstrates that regional scale variable density models are potentially useful tools for estimating rates of submarine ground water discharge.