The heavily industrialized lower reach of the Fox River, downstream of the DePere Dam, and lower Green Bay, Lake Michigan, are modeled. Hydrodynamics and contaminant transports to the bay are obtained from three-dimensional numerical models. The effect of outfalls located on the river is included in the analysis. Model results indicate that the contaminant transport in the river is dominated by: the dam outflow, which tends to slowly flush contaminants downstream through the river and into the bay; winds which vertically mix contaminants in the river and produce uniform vertical distributions; and bay seiche activity which delays loadings to the bay during half the seiche cycle then enhances it during the other half. Wind mixing, wind-generated currents, and seiching control contaminant transport in the lower bay.