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SAN JUAN PROGRAM ANIMAS LA PLATA BIOLOGICAL OPINION The San Juan Program originated from the reasonable and prudent alternative for the biological opinion on the Animas-La Plata Project (ALP), a federal reclama- tion project that was planned to ultimately deplete another 154,800 acre feet per year from the Animas and La Plata Rivers in Colorado and New Mexico, trib- utaries that join the San Juan River near Farmington. After surveys from 1987-1989 documented the sur- vival of a Colorado squawfish population in the main stem of the San Juan River below Farmington, the biological opinion for the ALP was re-opened and an extensive reasonable and prudent alternative was adopted in October 1991. This alternative presumed that if Navajo Reservoir, an existing federal water pro- ject further upstream on the San Juan River main- stem, was re-operated to mimic natural flow patterns, especially during the spring run-off, all existing deple- tions in the subbasin totalling some 566,000 acre feet per year plus another 57,100 acre feet of ALP munici- pal and industrial depletions would not jeopardize the likelihood of the survival of the Colorado squawfish. The BOR also agreed to fund seven years of research on the factors limiting recovery of the squawfish in the San Juan River, and on how best to modify the operation of Navajo Reservoir. Navajo Reservoir operations were then to be permanently modified based on this research. Despite a sharp protest from the SCLDF, this same reasonable and prudent alterna- tive was extended to the razorback sucker in December 1991, after its persistence in the lower ~ reaches and mouth of the Jan Juan River was docu- mented and the razorback was listed. The last element of this reasonable and prudent alterna- tive was that the modified releases of water from Navajo Reservoir be legally protected instream through the river reaches occupied by the listed fishes to mouth of the San Juan River. Because such legal flow protection was under the jurisdiction of the states of New Mexico, Utah, and Colorado, and the Navajo Nation, a Memorandum of Understanding (MOU) between these parties, plus three other participating tribes (the Southern Ute, Ute Mountain Ute, and Jicarilla Apache) and the Department of Interior (DOl) was a material condition to the biolog- ical opinion. Along with asserting their respective authorities to legally protect the Navajo Reservoir releases under this MOU, these parties were to develop a recovery implementation program within one year for the listed fishes in the San Juan River. SECTION 7 Consultations This MOU, which was signed by all parties except the Navajo Nation in October 1991 \ also outlined how Section 7 consultations will be conducted on water projects in the San Juan subbasin. Like the Upper Basin Program, making sufficient progress in the implementation of the San Juan Program, as detailed in its Long Range Plan, will constitute the reasonable and prudent alternative in these consultations, but the question of what constitutes sufficient progress is ulti- mately answered by the FWS. Like the Upper Basin Program, the magnitude of the impacts is an impor- tant factor and more progress is needed for larger 1 When the Navajo Nation decided not to sign this MOU and cast the viability of the ALP biological opinion in doubt, a supple- mental agreement was reached in among DOl, the state of Colorado, the two Ute Tribes in Colorado, two water district in Colorado, and a water commission to guard against the diversion of the Navajo Reservoir releases specified in the opinion or to replace them. 58