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EXECUTIVE StlHMARy The San Juan River is 'historic habitat for seven native fish species including three rare fish species: the Colorado pikeminnow (Ptvchocheilus lucius), razorback sucker (Xvrauchen texanus), and roundtail chub (Gila robusta) . Jeopardy opinions issued by the U. S. Fish and Wildlife Service (Service) during consultations on the Animas-La Plata (ALP) and Navajo Indian Irrigation Projects (NIIP) under Section 7 of the Endangered Species Act led to the initiation of a seven-year research period on the fish community of the San Juan River, beginning in 1991, The goal of this research period was to study the effects of test flows from Navajo Reservoir (upstream of Farmington, New Mexico {NM}) on the fish community and instream habitats in the San Juan River for the purpose of developing long-term flow recommendations for the permanent reoperation of Navajo Dam. AS part of these seven-year studies, the Servics's Colorado River Fishery Project (CRFP) office in Grand junction, Colorado (00) was given the lead responsibility for 'monitoring the response of the main channel adult fish community to test flows. The main objective of these test flows was to mimic, in shape, duration, and time (but not magnitude) a "natural" pre-Navajo Dam hydrograph and observe the effects this natural hydrograph had on the San Juan River fish community. Between 1991 and 1997 the CRFP office conducted a total of 26 electrofishing and numerous radiotelemetry trips in the San Juan River between the Animas River confluence (river mile {RM} 180.0; Reach 6) at Farmington, NM and Clay Hills Landing (RM 2.9; Reach 1) just upstream of Lake Powell in Utah (UT). Between 1991 and 1997, a total of 242,163 fish representing 26 species and three hybrid sucker forms were collected. Of the 26 species, 7 were native and 19 were introduced (nonnative) species. The three hybrid sucker forms included one native X native sucker hybrid and two native X nonnative sucker hybrids. Six species accounted for 99.1' of all fish collected during adult fish community monitoring (adult monitoring) trips. Three of these were native species (flannelmouth sucker, bluehead sucker, and speckled dace) and three were nonnative species (channel catfish {Ictalurus Dunctatus}, common earp {CVorinus carDio}, and red shiner {Cvorinella lutrensis}). The three most common nonnative species did not show a quantifiable negative response to test flows from Navajo Reservoir in main channel habitats. In fact, between 1993 and 1997 numbers of channel catfish and common carp increased in adult monitoring collections. It appears that with the amount of water presently available in the San Juan River, that populations of these three common nonnative fish species'can probably not be reduced or eliminated using flows from Navajo Reservoir alone. A drop in catch per unit of effort (CPUE; i.e., the number of fish per hour of electrofishing) observed for channel catfish and cOmmon carp in October 1997 versus previous trips may be linked to mechanical removal efforts that began on adult monitoring trips in October 1996' and took place on all subsequent trips. Notable among collections of nonnative fish species were the first scientifically~documented collections of a grass carp (CtenoDharvnaodon idella), and of white sucker (Catostomus commersoni) X flannelmouth sucker and white sucker X bluehead sucker hybrids from the mainstem San Juan River. Also notable among nonnative fish collections were the walleye, striped bass, and threadfin shad that invaded the lower San Juan River starting in the spring of 1995 when the waterfall at RM 0.0 became inundated by a rising Lake Powell. ii ..