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~ c-:.~ 1'-' EXECUTIVE SUMMARY i-Ol.'- t,,) .:> Between Shiprock, New Mexico and Chinle Creek, Utah, secondary channels are a common feature of the San Juan River. Prior to initiation of the San Juan River Seven- Year Research Program no studies specific to secondary channels had been conducted, As part of the Seven-Year Research Program, research was initiated in 1991 to characterize the fish fauna of San Juan River secondary channels, to discern seasonal-use patterns of secondary channels by common fishes, to evaluate the effects of different flow regimes on common fish species, and to characterize use of secondary channels by rare fishes (roundtail chub, Colorado pikeminnow, and razorback sucker). Summer inventories of secondary channels were iniliated in 1991 and spring and autumn invenlories began in 1993. Research on secondary channels occurred in Geomorphic Reaches 5, 4, and 3. Flows of 1500 cfs wetted most secondary channels and flows of 2500 cfs inundaled almost all. During spring, when flows were alleast 2500 cfs, native flannelmoulh sucker and bluehead sucker and nonnative common carp and channel catfish numerically dominated secondary channel fish collections, Small-bodied fishes such as native speckled dace and nonnative red shiner and fathead minnow, were uncommon in spring collections. The sampling technique, raft-mounted electrofishing, was not an effective means of collccting small-bodied fishes. Abundance of flannel mouth sucker was less in 1997 than 1993 in all reaches, but the decline was most apparent in Reach 4, Allhough abundance evidently declined, mean tolallength, mean biomass, size-struclure, and age-structure were not markedly differenl in 1997 from that found in 1993, Bluehead sucker abundance was least in 1995 in all Reaches and second greatest in 1997. Neither mean total length nor biomass was appreciably different in 1997 than that found in 1993, In Reach 5, where bluehead was typically most common, lhere was little change in size- or age-structure, but in Reach 3 (where least common), there was considerable variation in these populalion attribules among years. [n all years in all Reaches, most common carp captured were 2: 400 mm 10lallength and lhus adults. Common carp were slightly more common in all reaches in 1997 lhan 1993, bul mean total length and biomass did nol change, Abundance of channel catfish in Reaches 5 and 4 was slightly grealer in 1997 lhan 1993, but was considerably greater in Reach 3 in 1997 than 1993. Total biomass, however, was greater in 1993 lhan 1997 in Reaches 5 and 4, [n Reach 3, total biomass was least in 1993, but froml995 through 1997 did not change. Mean total length and biomass declined from 1993 lhrough 1997 in all reaches, but most dramatically in Reaches 5 and 4. Changes in size- and age-struclure of channel catfish were also noted; smaller and younger fish were more common in collections in 1997 than 1993. In most years (1994 lhrough 1997) and Reaches flannelmoulh sucker was slightly more abundant in secondary channels lhan the primary channel. Bluehead sucker, however, tended 10 be more common in the primary than secondary channels. In Reach 5, common carp were more common in secondary channels lhan primary chalmel in all years and usually so in