The Caloosahatchee Estuary is a large estuarine ecosystem, located on Florida's lower west coast, that supports a productive and diverse floral and faunal community. Major modifications to the hydrology of the Caloosahatchee watershed through water management, including water releases from Lake Okeechobee into the Caloosahatchee River, along with land-use transformations, increased development, and dredging for navigation, have resulted in alterations within the estuary. Changes in estuarine salinity, flows, and nutrient inputs, along with physical alterations to the estuary as a result of these stressors, can affect estuarine fishes and manatees, as well as benthic communities including several species of bivalves, such as oysters, scallops, and clams. Additionally, the submerged aquatic vegetation and mangrove shoreline habitat are affected through a variety of processes associated with these changes. As a result, these estuarine attributes can be used as indicators of restoration success.