The objective of this study was to develop a 3-D model for The Pontchartrain Estuary that was capable of long-term mass conservative simulation of salinities. This was accomplished in a multi-stage approach involving: a physical model of salinity exchange through a pass; a 3-D FVCOM model of the physical experiment; the development and testing of an FVCOM model for an idealized Pontchartrain Basin; and for the entire estuary. The data from the physical model tests were used to validate the performance of the FVCOM model with density-driven flows. These results showed that hydrostatic FVCOM captured the primary internal wave movement. The idealized basin simulations were used to evaluate several issues related to salinity transport, namely the relative importance of baroclinic forcing, tidal forcing and hydrology. The idealized domain also permitted the testing of sigma-gradients, spatial distribution of friction coefficients, wind stress and various boundary treatments. The results showed that the density-driven exchange of saltwater at the open boundary required a baroclinic boundary condition for salinity as well as a lateral filter at the boundary on each sigma layer. A new radiative baroclinic open boundary condition was developed for FVCOM. When tides and hydrology were included, the FVCOM model was shown to reproduce the seasonal salinity that has been observed for long-term periods. It was also found that the simulation of tides and salinity in FVCOM is very sensitive to the spatial distribution of the friction coefficient; relatively low friction was required in the open water regions and high friction was needed in the passes and waterways to reproduce the tides and salinity distribution. A variable friction coefficient option was coded on FVCOM. The findings from the idealized model were utilized to setup two models for the actual estuary. Both models extend from Lake Maurepas, one to the Chandeleurs Islands and the other to Mobile Bay. The baroclinic open boundary and variable friction were implemented in these models. They were calibrated for tides and salinity. The 2008 Bonnet Carré Spillway Opening was applied to the first model. A tidal pumping effect in Lake Pontchartrain was observed and captured by the model.