The Salt River basin drains 2,914 square miles of northeastern Missouri covering all or part of twelve counties (Adair, Audrain, Boone, Calloway, Knox, Macon, Monroe, Pike, Ralls, Randolph, Schuyler, and Shelby; Figures Lo01, Lo02, Lo03). The longest stream in the basin is the North Fork Salt River which originates in Schuyler County and flows southeast approximately 119 miles until meeting the South Fork Salt River in Mark Twain Lake. Major streams in the North Fork sub-basin include Bear Creek, Otter Creek, Crooked Creek, Black Creek, TenMile Creek, Titus Creek, and Floyd Creek. The South Fork Salt River originates in Audrain County and flows north approximately 68 miles. Middle Fork Salt River, the largest South Fork tributary, begins in Adair County and flows southeast about 116 miles before meeting the South Fork in Mark Twain Lake. Principal streams in the Middle Fork sub-basin include Elk Fork, Bee Creek, Allen Creek, Milligan Creek, Flat Creek, Mud Creek, Hoover Creek, and Narrows Creek. Other major streams in the South Fork sub-basin include Long Branch, Brush Creek, Youngs Creek, Littleby Creek, Skull Lick Creek, Davis Creek, and Beaverdam Creek.
The lower Salt River begins at the confluence of North Fork and South Fork. The first 15 miles are impounded by Clarence Cannon Dam which was completed in 1983 to create Mark Twain Lake. This dam is located about 63 miles upstream from the Salt River's confluence with the Mississippi River at River Mile 284. The Salt River is also regulated for another 9.5 miles downstream of Clarence Cannon Dam by a re-regulation dam. The total length of Salt River from its mouth to the upper forks is 78 miles. Principal streams of the lower Salt River that flow directly into Mark Twain Lake are Lick Creek, Indian Creek, and Little Indian Creek. Major streams in lower Salt River watershed below the re-regulation dam include Spencer Creek, South Spencer Creek, Sugar Creek, and Peno Creek.
The Salt River basin is bounded by the North River and Fabius River basins to the northeast, the Chariton River basin to the west, and by several Missouri River drainages and the Cuivre River basin to the south.
Prior to the construction of Mark Twain Lake by the U.S. Army Corps of Engineers, the Salt River was surveyed in detail by numerous agencies. An environmental assessment was conducted by Missouri Botanical Gardens (Klein and Daley 1974), a final environmental statement (1975) and a preimpoundment water quality report (1974) were prepared by the St. Louis District of the U.S. Corps of Engineers, and a biological study was conducted by Environmental Science and Engineering, Inc. (Govro 1984). Much of the background and historical information presented in this document were obtained from these references.