A high-resolution, three-dimensional, hydrodynamic model of the Duplin River estuary on Sapelo Island Georgia has been developed using Finite Volume Community Ocean Model. Using a model to describe transport and retention is a good way to estimate the efficiency of an estuary at remediating contaminants. The model shows good agreement with time series of sea surface height and salinity from monitoring stations within the domain. The model does well at predicting tidal oscillations and subtidal SSH and salinity variations. However, there is room for improvement with regard to salinity variability in the upper model domain. A Lagrangian particle tracking analysis was carried out to study the effects of semi-diurnal tides, spring/neap tidal cycles, and seasonal forcings on residence times. Residence time is most sensitive to the stage of the tide (slack high or slack low) when starting the particle tracking and had maximum values on slack low water. Neap tides had characteristically longer residence times than spring tides. Residence time was also dependent on seasonal changes and was higher during periods of low river discharge which correspond to higher sea surface inundation than periods of high river discharge. An Eulerian salt flux analysis was carried out to study the relative roles of advective and dispersive flux on transport processes. The residual or advective flux, dominates the transport within the system and marsh circulation in the upper reaches shows net inward movement along the channel and net outward movement over the marsh. Tidal flux dominates the dispersive flux over estuarine exchange flux and thus controls the horizontal dispersion. The horizontal dispersion coefficient was dependent on seasonal river discharge as the horizontal salinity gradient switches from a positive to a negative estuary causing very large and highly variable values during periods of high river discharge. Alternatively, the horizontal dispersion coefficient was more periodic and controlled by the spring/neap cycle, showing maxima on spring tides during the season of low river discharge and high sea surface inundation.