The study described here is a subset of a broader climate-related study, and is focused primarily on salinity intrusion into Delaware Bay and River. Given changes in freshwater discharge into the Delaware River as determined from the larger study, and given probable sea level rise estimates, the purpose here is to calculate the distribution of salinity within Delaware Bay and River. The approach adopted for this study is composed of two parts: an analysis of existing physical data in order to derive a basic understanding of the salt dynamics, and numerical simulation of future conditions based on this analysis. There are two important constraints in the model used: it must resolve the spatial scales important to the salt dynamics, and it must be sufficiently efficient to allow extensive sensitivity studies. This has led to the development of a 3D model that uses harmonic decomposition in time and irregular finite elements in space. All nonlinear terms are retained in the governing equations, including quadratic bottom stress, advection, and wave transport (continuity nonlinearity). These equations are coupled to the advection-diffusion equation for salt so that density gradient forcing is included in the momentum equations. Although this study is still in progress, the model has reproduced sea level variations and the 3D structure of tidal and residual currents very well. In addition, the study has addressed the effects of a 1-meter rise in mean sea level on hydrodynamics of the study area. Current work is focused on salt dynamics.