The Pawnee Watershed District had its beginnings in 1965 when a group of interested farmers and businessmen met together to form a steering committee to explore the formation of a watershed district. A vote to organize the District passed overwhelmingly. The District received its corporate charter in 1968, organized under the Watershed District Act of Kansas.

The District is the largest watershed district in the United States, containing more than 1.5 million acres in parts of nine southwest Kansas counties-Edwards, Finney, Ford, Gray, Hodgeman, Lane, Ness, Pawnee, and Rush. Governance is by a nine-person Board of Directors, with a member each from the seven subwatersheds, and two at-large members.