The South Shore Esutary Reserve Comprehensive Management Plan offers recommendations to incorporate an ecosystem perspective into the management of the Reserve's living estuarine resources; to increase wetland community values; to recognize, restore and protect tributary-based resource values; to protect and improve habitat conditions for estuarine bird species; to improve the productivity of important living resources; and to address scientific information needs.
Human population growth and burgeoning development in the Reserve, especially since World War II, had and continues to have a dramatic effect on the estuary. Most habitat loss in the Reserve has been the result of the filling of low-lying lands in the western portion of the Reserve for residential and commercial uses. Other development activities, including construction of canals, roads and bridges, have also destroyed or degraded habitats. According to the NYS Department of Environmental Conservation 1996 Priority Waterbody List, stormwater polluted by elevated levels of fecal coliform bacteria, excessive nutrients and sediment has affected the viability of fish populations in the Reserve's tributaries and has closed almost 31,000 acres of hard clam beds in its bays. 
