With limited funds available for restoration and management, information is needed that would enhance the objectives of restoration of the eastern oyster (Crassostrea virginica) in Chesapeake Bay. One challenge with choosing locations for C. virginica restoration is lack of information regarding larval exchange, which helps determine whether the reefs will be self-sustaining and/or enhance nearby populations. The goal of this research was to estimate the larval exchange between subpopulations within the Choptank and Little Choptank Rivers (Maryland, USA) and to determine the influence of low salinity on these patterns in connectivity. To this end, the Lagrangian TRANSport model (LTRANS) was coupled with a Regional Ocean Modeling System hydrodynamic model of Choptank River (ChopROMS) and applied to predict the exchange of simulated C. virginica larvae between 596 reefs within the system. Model results indicated that there is a high degree of connectivity among the subpopulations in this system. Most simulated larvae were transported down river (rather than upriver). Reefs in upper portions of the Choptank River and its tributaries were in a position to produce the most larvae which encountered suitable habitat, whereas those in the lower Choptank River received the most simulated larvae. In addition, salinity-induced mortality of larvae substantially decreased transport success and self-recruitment, and changed patterns in reef-specific transport success throughout the estuary. Model results provide region-specific information that could be used to support restoration efforts in areas with low salinities like the Choptank River.