Estimating groundwater flows in karst-dominated landscapes is difficulted by the lack of observed groundwater flows and the uncertainty in hydrogeological parameters (hydraulic conductivity, specific storage and yield, porosity, anisotropy, etc.). The State of Florida (USA) landscape is dominated by the largest geographic area of geologically young carbonate and rocks with well-developed karst features in North America. In this research, a MODFLOW groundwater model for central Biscayne Bay is presented. The Bay is surrounded by karst terrain. The groundwater model is loosely linked to a hydrodynamic model to estimate salinity concentrations at the Biscayne Bay's central coast. The loose-link model framework is shown to improve salinity estimations in 50% from estimations that do not include groundwater contributions to the Bay. A statistical comparison of simulated concentrations versus observed data demonstrates that the loose-link model simulates salinity concentration values and trends within acceptable margin of errors (0.72 < R < 0.77; 0.52 < R-2 < 0.59; 0.62 < K-G < 0.70; d > 0.76; 4.1% < PBIAS < 13.5%). These results have the potential to be applied to other coastal locations in Florida and the world where karst terrain is predominant.