Extensive modifications of river systems have left floodplains some of the most endangered ecosystems in the world and made restoration of these systems a priority. Modified river ecosystems frequently support invasive species to the detriment of native species. Rana catesbeiana (American bullfrog) is an invasive amphibian that thrives in modified aquatic habitats. In 2004–2005 we studied the distribution of bullfrogs along a 98-km reach of the Trinity River below the Lewiston Dam to identify habitat characteristics associated with bullfrogs and to recommend actions to reduce their prevalence in the system. We also examined native amphibian distributions relative to bullfrogs and disturbance regimes. We used regression techniques to model the distribution of bullfrogs in relation to environmental conditions. Models assessing breeding habitat outperformed models assessing bullfrog presence. Top-ranked predictor variables of bullfrog distribution included water depth, percent rooted floating vegetation, and river km. Most breeding sites of bullfrogs were relict mine tailing ponds or inactive side channels created during restoration activities in the 1990s. Native species were more common in the lower reach where habitats were less modified, in contrast to the distribution of bullfrogs that dominated the upper, more modified reach. To control bullfrogs along a managed river, we suggest reducing the suitability of breeding sites by decreasing depth or reducing hydroperiod and increasing connection with the active river channel. Current management goals of restoring salmonid habitat and returning the river to a more natural hydrologic condition should aid in control of bullfrogs and improve conditions for native amphibians.