The Upper Choctawhatchee is composed of the main channel, the West and East Forks of the Choctawhatchee and 24 major tributaries. The main channel is approximately 90 miles long.(GSA)

Upper Choctawhatchee Tributaries
Barnes Creek, Bear Creek, Beaverdam Creek, Bell Creek, Blackwood Creek, Bowles Creek, Claybank Creek, Double Bridges Creek, Hurricane Creek, Judy Creek, Lindsey Creek, Little Choctawhatchee River, Little Double Bridges Creek, Little Judy Creek, Newton Creek, Panther Creek, Pates Creek, Pea River, Piney Woods Creek, Poor Creek, Skies Creek, Steep Head Creek, Tight Eye Creek, Wilkeson Creek.

There is a proposed regional drinking water reservoir proposed for the Little Choctawhatchee River that drains west Dothan and joins the mainstem on its eastern bank. 

Double Bridges Creek runs just north of Geneva and meets the Choctawhatchee on its western bank just upstream of its confluence with the Pea. In addition to some pollution problems, this stream has contributed to flooding damages to the city of Geneva. (Troy and NRCS)

The Pea River, the largest tributary of the Choctawhatchee, is formed in Bullock County southeast of Union Springs and flows generally southwest for about 128 miles to join the Choctawhatchee near Geneva in Geneva County a short distance north of the Florida line. The Pea River subwatershed encompasses 1,542 square miles and sits just west of the Choctawhatchee mainstem. It flows 68 miles to Elba, then south for about 30 miles to the west of Samson, then gradually turns east and dips slightly into Florida before joining the Choctawhatchee River at mile 91.7 south of Geneva. 93% of the subbasin is in Alabama and 7% in Florida. (Corps)

Fisheries in the Pea were assessed by Scott Mettee in 1970. He found 47 of the total 129 species found in the Choctawhatchee basin. The Pea is the only habitat for the green sunfish in the basin. (Corps)

Pea River tributaries
Beaver Dam, Big Creek, Big Sandy Creek, Bluff Creek, Bowden Mill Creek, Buckhorn Creek, Bucks Mill Creek, Eightmile Creek, Flat Creek, Hays Creek, Holly Mill Creek, Little Indian Creek, Mims Creek, Pages Creek, Panther Creek, Pea Creek, Perote Creek, Richland Creek, Sandy Creek, Silers Creek, Stinking Creek, Walnut Creek, Whitewater Creek. 

Flat Creek contains perhaps the most diverse mussel fauna of any section in the Choctawhatchee Basin accounting for 15 of the 21 species found. One species (Utterbackia peggyae) is found nowhere else in the watershed.

Big Creek and Whitwater Creek are significant tributaries to the Pea that orginate just below Troy, AL

The Choctawhatchee Bay is 25 miles long running east to west with an average width of 3 miles. It rests 40 miles east of Pensacola and 30 miles west of Panama City. It has a surface area of 86,000 acres with an average depth of 10 feet in the eastern 1/3 and 30 feet in the remainder. The bay has only one narrow channel to the Gulf of Mexico called the East Pass. 

Choctawhatchee Bay and Santa Rosa Sound are sandy, shallow, greenish-brown expanses of brackish water surrounded by marsh grasses and oyster beds.  At the east end of the bay, the Choctawhatchee River winds its way through a swamp to dump its tannic stained water into the bay.  At the west end of the bay, Santa Rosa Sound connects the bay to Pensacola Bay, as a 40 mile long saltwater river that daily reverses course on the tide change.  At the south end of the bay is the Destin Pass into the Gulf of Mexico.   The arrangement of these passes and saltwater channels forces large shifts in the salt concentrations of the bay on each tide, making the growth of some type of sea grasses impossible.

As a result only patches of brown sea grass grow underwater and only in shallow flats on the bay, and small patches of oyster beds grow, leaving  much of the bay bottom  bare mud&sand.  As a result, aquatic life in the bay hugs the marshes on the edges of the bay, around bridges/pillings and piers, and around these patches of grass and oysters.  The large fishes, which cannot always hug this sparse cover, hug drop offs and tide current edges in the passes and channels.

For tributaries for the lower Choctawhatchee Basin in Florida see EPA websiste or NRCS report.