Since the lower Savannah River Estuary was first settled in 1733, shaping and deepening the river channel to provide easy, safe access to the sea has been a near continuous effort. Once averaging about 3 m in depth, the channel is now over 12 m deep, and currently there is an investigation evaluating a further deepening of up to 2 m. These modifications to the estuary have not been without unintended environmental consequences. The saltwater-freshwater interface has moved nearly 25 km upriver since it was first measured in the 1700s. In 1977, saltwater intrusion was exacerbated by the operation of a tide gate in the Back River channel of the estuary. Salinity increase d in the Savannah National Wildlife Refuge and converted much of the tidal freshwater marsh to less des irable brackish and saline marsh. Further, the salinity shift affected the freshwater spawning and nursery grounds of the striped bass Morone saxatilis. As a result, striped bass reproduction declined by 96% and adult striped bass abundance declined by 97%. Restoration efforts (which included stock enhancement and habitat mitigation) have resulted in increased striped bass adult abundances and increased egg production. Previous studies concluded that restoration of the Back River, considered the primary striped bass spawning ground, was paramount and would allow latitude for additional harbor developm ent. However, use of egg surrog ates to evaluate sampling efficiency has led to the discovery that sampling biases may have fostered faulty conclusions: historic egg abundance has been at least an order of magnitude greater in the Front River than in the Back River. We now know we must regard the estuary as a whole system, rather than as individual reaches. Considering this, and the currently proposed deepening, models were employed to evaluate the effect of increased salinity on striped bass eggs and larvae immediately upstream of the harbor. Deepening scenarios that result in upstream isohaline shifts greater than 2 km will have significant impacts on striped bass recruitment potential. Overall, the striped bass population appears to be recovering, although the prospect of additional deepening m ay threaten tha t recovery.