The Bureau of Reclamation consulted with the U.S. Fish and Wildlife Service between 1991 and 1997 to develop operation criteria at Navajo Dam that would comply with the Endangered Species Act. Since 1999, Navajo Dam releases have been changed to approximate the historic seasonal hydrograph of the San Juan River, rather than a stable flow year-round. The San Juan River Basin Recovery Implementation Program requires spring peak releases of , dependent on water availability, and a reduction of the summer base flow from to , to mimic historic dry season conditions. The peak release from Navajo Dam is timed to match the peak of snowmelt runoff on the Animas River. The program also includes other restoration and remediation work, such as improving fish passage at diversion dams, removing obsolete diversion structures, and eradication of non-native species such as catfish.