Opening the gate leading from the Rio Grande, Doña Ana County, New Mexico, 1936. Library of Congress, Prints & Photographs Division, FSA-OWI Collection, No. fsa 8b27361
The history of the Paso del Norte Watershed Council begins with the formation of the New Mexico-Texas Water Commission ("Commission") in 1991. The Commission's purpose was to develop a 50-year water supply plan for the region of southern New Mexico and El Paso, Texas. An environmental impact study (EIS) was required for the El Paso-Las Cruces Regional Sustainable Water Project ("Project"), and several mitigation and river enhancement projects were identified. As a result, the EIS states that 2 percent of funds raised for construction projects associated with the Project are to be set aside for ecological improvements to the river.

The Commission recognized the need for a group that would select the appropriate restoration projects and facilitate their implementation. A watershed council planning committee formed in January 2000, and over the next ten months developed organizational documents like a strategic plan. On October 13, 2000, the Commission passed a resolution forming the Paso del Norte Watershed Council. The Council held its first meeting in January 2001. Since that time, the Council has met an average of 7 times each year.

In August 2002, a Cooperative Agreement was entered into between El Paso Water Utilities (EPWU), on behalf of the New Mexico-Texas Water Commission, and the Texas AgriLife Research and Extension Center (formerly El Paso Agricultural Research and Extension Center/Texas Agricultural Experiment Station), on behalf of the Council. This initiated the first phase for the development of a Coordinated Water Resources Database and Geographic Information System Project (CDP Project). The CDP Project is a system that provides the river flow and water quality with as much "real-time" information as possible. Continuation of the CDP Project has occurred through 2011 and has been made possible with funding from EPWU, the U.S. Army Corps of Engineers, and the U.S. Bureau of Reclamation in parallel to development of surface water flow model for flood control and water operations planning.