The exchange of dissolved constituents between a shallow bay and the ocean is governed by regular tidal fluxes as well as by wind generated storm surges and currents. In this study the transport of a conservative tracer was simulated using the numerical model Delft3D in a system of shallow bays along the coast of the Delmarva Peninsula, Virginia. The evaluation of the tracer residence time was carried out using the Eulerian approach. The main mechanisms governing the decay of the tracer concentration inside the lagoons were assessed by considering the influence of different factors such as the time of release of the tracer with respect to the tidal cycle, tidal amplitude, and local winds. The exponential curve well approximates the decay of the tracer concentration in time. A set of simulations shows that the prevailing factor controlling the tracer transport and, therefore, the tracer concentration within the lagoons are wind-driven fluxes. Large tidal amplitudes also promote the flushing of the tracer out of the bay, while the time of tracer release with respect to the tidal phase has been found to play a relatively negligible role. Finally, a simplified approach is presented to compute the decay of tracer concentration in time. The method accounts for hourly variable wind characteristics as well as seasonal changes in meteorological conditions.