Hog Island Bay, Virginia, is a shallow back barrier lagoon that is subject to seasonal inputs of inorganic nitrogen and related episodes of hypoxia. Numerical simulations were carried out to estimate the importance of physical flushing times relative to biochemical turnover times known to be a few days or less within the system. A 2D vertically averaged finite element hydrodynamic model, which was designed to accommodate regular flooding and dewatering of shallow flats and marshes, was coupled with a particle tracking model to estimate median lagoon residence time and the spatial distribution of local residence time in the lagoon. The model was forced with observed tidal elevations and winds from the end of the growing season when hypoxia tends to occur. The median residence time estimated by numerical modeling is on the order of weeks (358 hours), and variations in tidal stage, tidal range and wind produced deviations in median residence time on the order of days. Residence times near the inlets were very short, while those near the mainland were long, showing that (i) horizontal mixing in the Bay is insufficient to successfully apply integral methods to obtain residence times, and (ii) residence times near the mainland are long compared to timescales of biologically driven chemical transformations.