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560 SAN JUAN RIVER SECONDARY CHANNEL COMMUNITY DYNAMICS STUDY 1997 WORK PLAN New Mexico Department of Game and Fish, Santa Fe, New Mexico Background: Ichthyofaunal inventories of the San Juan River found differences between the fish communities of secondary and primary channels. Differences were noted in species present, their relative abundance, and life stages present. - These differences were hypothesized to be mediated in part by differences in habitat available at various river flows. Seasonal inventories of secondary channels were initiated in 1992. These inventories occurred from the Hogback Diversion or Shiprock, New Mexico downstream to Bluff or Mexican Hat, Utah and were conducted during spring (high flows), summer (low flows), and autumn (low to intermediate flows). In addition to detecting seasonal differences in community composition, the inventories found species-specific longitudinal abundance patterns within seasons. These findings prompted initiation (1993) of intensive studies on four secondary channels that, among them, were representative of the array of secondary channels in the San Juan River. These studies indicated that high spring flows serve to annually "reset" the fish community of secondary channels. During spring runoff the fish community is largely composed of native fishes. As runoff recedes, nonnative fishes progressively become more abundant and by late summer and early autumn numerically dominate, by a large margin, secondary channel fish communities. The most common nonnative fishes are red shiner and fathead minnow. With the onset of spring runoff, nonnative fishes decline in abundance. The reproductive biology of each species, the "preferred" habitat of each, relative resistance of each to displacement by elevated flows, thermal and oxygen-depletion stress tolerances, and food habits may influence documented changes in secondary channel fish community structure. After cessation of spring runoff, secondary channel habitats are largely slow velocity runs and shallow pools. Such habitats represent a low proportion of that associated with the primary channel. Low-velocity habitats, particularly backwaters, are believed to be essential to survival of Age 0 Colorado squawfish. To date, no young Colorado squawfish have been collected in secondary channel habitats. The extremely high abundance of nonnative species, such as red shiner, may be a factor or secondary channel habitats may lack some attribute necessary for young Colorado squawfish. Young roundtail chub, however, were collected in secondary channel habitats, indicating there is suitable habitat for this species. To test the influence of elevated summer flows on nonnative fishes in secondary channels, the Biology Committee requested that summer releases from Navajo Reservoir during 1995 be maintained at 800 cfs rather than the "normal" 500 cfs. During summer 1996, flows were average to below average. During fiscal 1996 (1 October 1995-30 September 1996), three secondary channel inventories between Shiprock, New Mexico and Bluff, Utah were made. All sampling was done per protocols outlined in previous work plans. Lateral movement of the primary channel eliminated the permanent secondary channel study site located near Bluff, Utah_ Regular sampling of the other three permanent secondary channel study sites, however, continued per study protocol. 20