Bayhead deltas exist between the fluvial and central-basin depositional environments of many incised-valley-fill successions. Prior work has shown that tributary junctions in flooded incised valleys provide “pinning points” or locations of stabilization for bayhead deltas during transgression. The purpose of this study is to examine the influence of tributary junctions on the behavior of bayhead deltas during regression. This influence is examined by using a simple numerical model that incorporates established relationships for systematic changes in valley geomorphology downstream. In addition, the model incorporates important observations regarding the controls on water depth in wave-dominated estuarine central basins, which in part controls sediment accommodation. Water depth in the central basin of wave-dominated estuaries with high suspended sediment loads is a function of the width of the central basin parallel to the prevailing wind direction (fetch). A direct relationship is observed between the width of the central basin parallel to the prevailing wind direction and water depth based on data from modern estuaries in North America, Europe, and South America. Our model shows that bayhead-delta progradation rates increase at tributary confluences and larger deltas prograde at faster rates than smaller deltas. In the case of two tributary bayhead deltas fed by systems of the same size coming together, the combined bayhead delta progrades 17.6% faster. This study provides one more example of the importance of autogenic processes in influencing stratigraphic architecture and the rate of shoreline changes.