We quantified the availability and utilization of habitat types by eight small-bodied cyprinid fish species, including the federally threatened Pecos bluntnose shiner Notropis simus pecosensis, in the Pecos River, New Mexico. The Pecos River is a medium-sized, sand-bed river with a highly variable hydrograph and some reaches characterized by historic and recent periods of flow intermittency. Fish habitat was described in four reaches at flows of 0.05-2.29 m(3)/s by means of a simultaneous, coordinated program of channel topographic surveys, mesohabitat mapping, fish sampling, and measurement of microhabitat and chemical parameters. We determined that fish habitat in this sand-bed river was effectively described at the mesohabitat scale. Furthermore, mesohabitats were visually distinguishable and separable by means of hydraulic and geomorphic parameters and the relationship between flow and depth, velocity, and velocity: depth ratios. The eight cyprinid species in the Pecos River primarily used four mesohabitat types that were consistently available at the full range of flows examined, including perpendicular and parallel plunges, backwaters, and slackwaters. In winter, five species (red shiner Cyprinella lutrensis, plains killifish Fundulus zebrinus, plains minnow Hybognathus placitus, Arkansas River shiner N. girardi, and sand shiner N. stramineus) shifted to backwaters, where water temperatures were relatively warmer than those of the main channel. Runs, flats, and riffles were generally the most available mesohabitat types, but their availability changed with flow; only four species (red shiner, plains killifish, speckled chub Macrhybopsis aestivalis, and sand shiner) selected these types, and they did so infrequently in summer. The Pecos bluntnose shiner was a habitat specialist that selected primarily rare plunge pools at sandbar faces, whereas species such as the red shiner were habitat generalists that used a variety of mesohabitat types. We found that a range of base flows sustained the preferred habitats of the eight cyprinid species and that no single flow maximized this preferred habitat because of a scaling effect of flow on sand bedforms.
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