In Part 2 of our application of the Navy coastal ocean model (NCOM) to the Atchafalaya Bay system, we examine the wind- and tide-forced three-dimensional baroclinic circulation of the Lower Atchafalaya and Wax Lake Outlet river plumes. The salinity and the current velocity are examined during a time period when three cold fronts passed over the region. The baroclinic circulation of NCOM was validated for the same time period in Part 1 of this study (Cobb, Keen, and Walker, 2008. Modeling the circulation of the Atchafalaya Bay region, 1: Model description and validation. Journal of Coastal Research, this issue). We find that the westward transport of plume water and the offshore cold-front–induced circulation are determined to a large extent by the alongshore and cross-shore bathymetric structure. Wind-driven plume water moves parallel to the alongshore bathymetric contours unless forced to mix with higher salinity water by strong cross-shore directed winds. The mixing of plume water with offshore water occurs over bathymetric shoals during periods of strong post-frontal winds. This mixing process involves the offshore transport of plume water over the entire water column in addition to the strong surface transport. The model results for offshore circulation are in qualitative agreement with past observations. In addition, the hydrodynamic processes that control the salinity fronts in Vermilion and West Cote Blanche Bays, areas where the model salinity was validated in Part 1, are examined as well.