The process of preserving species diversity through large scale habitat protection favors the listed species of the Charlotte Harbor National Estuary Program study area. The most critical use of Charlotte Harbor, for numerous species, is a protected nursery area for both larval and juvenile stages of fish. The Harbor is internationally famous for sea shelling, tarpon tournaments, and snook fishing. Many varieties of wildlife and plants are found in this area as well. Manatees, sea turtles, wood storks, and dolphins are watershed inhabitants.
Mangrove trees line the shore and provide important habitat for fish, birds, and other wildlife.
Rapid urban development has radically changed the character and ecology of river mouth and coastal waters. Mangroves have been removed or cut back, red tide events cause public health warnings, seagrass areas have declined or have been damaged, and groundwater pumping has reached its maximum limit. Although the main body of Charlotte Harbor and its adjacent estuarine systems are in comparatively good condition compared to severely damaged areas, the watershed reflects the pressure of human activities. If the watershed's population continues to grow at predicted growth rates, these pressures must be addressed to prevent further threats to natural systems and to protect current uses of resources. Management challenges to the local communities include managing mangrove areas, protecting seagrass areas from boat damage and water pollution, securing new water supply sources for growing populations and businesses, managing waste generated by septic tanks and sewer outfalls, protecting wetland areas for water retention, groundwater recharge, and wildlife habitat, and improving the efficiency of freshwater usage.