The federal Water Resource and Development Act of 1986 authorized the Secretary of the Army to undertake measures necessary to preserve and restore the diversion structures and associated canals of acequias. Under both the Section 215 and 1113 Programs, the federal government funds 75 percent of total project costs. The annual federal funding for Section 215 and 1113 Programs, routed through the U.S. Army Corps of Engineers, ranges from approximately $1.5 million a year to approximately $5 million a year. The Commission provides 17.5 percent of the total cost, and the acequia association provides 7.5 percent of the total cost.

Under the Section 113 Acequia Program, the Corps is responsible for all design, National Environment Policy Act (NEPA) compliance activities, real estate easements, advertisement of the construction bids, contract awards, construction inspection and oversight, and project financial management. In the Section 215 Acequia Program, the acequia controls design and construction, normally using Commission and NRCS assistance and expertise. NEPA compliance activities, usually consisting of simple environmental assessments, remain the responsibility of the Corps.

Under the Corps 215 Program, the acequia manages construction activities. Project designs are typically completed by the Natural Resource Conservation Service under the New Mexico Interstate Stream Commission Technical Assistance Program. NEPA compliance is managed by the Corps.