The Land Acquisition program of the Northwest Florida Water Management District is driven by the District's continuing commitment to permanently protect and preserve the water resources of northwest Florida. This program continues to build upon the more than 179,000 acres of wetlands and recharge areas already acquired by the District since it began its land acquisition efforts in 1984. At present, some 2.5 percent of the District's total land area of 7,168,000 acres is protected explicitly for water resource purposes by lands the District has acquired.

The Choctawhatchee Coastal Conservancy is a local 501(c)(3) non-profit land trust established in 1999 whose stated purpose is the acquisition, holding, and managing of environmentally sensitive lands and archaeological sites; the establishment of nature preserves and native habitat sanctuaries for ecological, scientific, educational, cultural, aesthetic, historic, scenic or open space opportunities; the scientific study, protection and preservation of native marine, estuarine, littoral, sylvatic and miscellaneous other natural communities together with all individual living entities contained therein; and the protection and care of imperiled, abused, threatened or endangered individual animals, creatures, or otherwise threatened organisms. The Choctawhatchee Coastal Conservancy emphasizes the importance of also preserving less known and smaller but ecologically significant lands, which are often disregarded by larger organisations and funding sources.

The Choctawhatchee Basin Alliance is a partnership of citizens, agencies, and local businesses organized to promote ecosystem management and sustainable development for Choctawhatchee Bay and its watershed. Their offices are located in Destin, Florida.

The Choctawhatchee-Pea Rivers Improvement Association was formed January 30, 1989, by a group of citizens concerned with developing the natural resources of the Choctawhatchee and Pea Rivers. In December of 1989, the organization filed a petition for the creation of a conservancy district. The association became the Choctawhatchee-Pea Rivers Conservancy District. In May of 1991, the Alabama Legislature passed Act 91-602 authorizing the establishment of watershed management authorities with the intent of protecting and managing the watersheds of the State of Alabama. The Choctawhatchee-Pea Rivers Watershed Management Authority became the first watershed management authority created under this law in Alabama. It remains the only authority in the state as of October 2001.

The Choctawhatchee-Pea Watershed Management Authority is charged with the responsibility in matters relating to water conservation, water usage, flood prevention, flood control, water pollution control, habitat protection, agriculture and erosion control. These are arranged into four management elements 1)water quantity, 2) water quality, 3) flood control, 4) education. The Authority won a Gulf Guardians Award and has received national acclaim for their recent Unpaved Road and Erosion and Sediment Control Project.(CPRWMA-plan)

The Alabama Environmental Council recognizes the Choctawhatchee River as one of ten Natural Wonders that represent the scenic and ecological diversity of Alabama.

The Natural Resources Conservation Service and the Alabama Forestry Commission both have field personnel that assist in the implementation of conservation practices to reduce soil erosion and improve water quality.