1. Fish assemblages and habitats were sampled annually at fixed sites in three tributaries of the Gila River catchment over a 21-year span that included prolonged low- and high-flow periods. Model selection was used to evaluate responses of seven native fishes with variable ecological traits (four small-bodied cyprinids, one large-bodied cyprinid, and two large-bodied catostomids) to mean annual discharge and predacious non-native fishes across the three sites. We also compared habitat use and overlap of native and non-native fishes to identify potential for negative interactions among species.
2. Assemblage structure (species abundance and richness) and recruitment of native species was strongly and primarily affected by mean annual discharge and secondarily by location and densities of non-native predators (mainly the centrarchid Micropterus dolomieui).
3. Densities of age-0 catostomids and small-bodied cyprinids were positively associated with discharge, and this pattern was strongest in the tributary with the lowest densities of non-native predators. Absence or extreme low abundance of natives during low-flow years was most pronounced at the sites where non-native predators were comparatively common. Densities of adults of large-bodied native species also varied by site, but often were positively associated with densities of non-native predators.
4. Spatially variable responses of native fish assemblages indicated that the persistence of native fishes could be jeopardized if key habitats were lost or flow regimes unnaturally altered, particularly during low-flow conditions when recruitment of native fishes is low and predation by non-natives is high. Large-bodied species may be less vulnerable to multiple years of poor conditions because adults are able to avoid predation by non-natives and thus can rely on occasional high discharge years for successful recruitment.
5. As in other arid-land streams, native fish assemblages of the Gila River Basin continue to decline. Our results indicate that conservation requires specific knowledge and consideration of physical influences as well as life-history attributes of native and non-native fishes.