We report results from a 3-year field investigation to limit hybridization between native and nonnative suckers in 2 small tributaries of the Gunnison River basin, Delta County, Colorado. Upstream movement to spawning habitat was selectively impeded by picket weir in intermittent Cottonwood Creek. There, native suckers were identified based on morphological characters in the field and were transferred upstream of the weir, whereas nonnative fishes were excluded from upstream movement. Another stream, Potter Creek, was not impeded by weir. Genetic identification of adult fishes in both streams was consistent with morphological identification in the field. Larval genetic identification was consistent with probable spawning species in Potter Creek. However, in Cottonwood Creek, larval fish proportions differed significantly from likely spawners. Proportions of nonnative suckers were high in Cottonwood Creek because exclusion structures were compromised by flooding during the spawning season. Yet, instream control of spawning by nonnative fishes has potential for reducing the incidence of hybridization, but practical challenges remain for implementation in the field.