We sampled nonnative fishes stranded in isolated pools near Grand Falls in the Little Colorado River (LCR), Arizona, after the river ceased flowing (21 June and 12 July 2005) to evaluate whether nonnative fishes can invade the perennial, lower 21 km of the LCR from upriver sources. The encroachment of nonnative fishes could jeopardize resident populations of endangered humpback chub, Gila cypha, and other native fishes in the lower LCR. We captured red shiner, Cyprinella lutrensis; common carp, Cyprinus carpio; fathead minnow, Pimephales promelas; black bullhead, Ameiurus melas; and plains killifish, Fundulus zebrinus, all of which have been captured >132 km downriver in the lower LCR and >127 km upriver in the closest perennial sources. Moreover, we detected Asian tapeworm, Bothriocephalus acheilognathi, in 9 of 30 common carp examined. Our findings suggest that nonnative fishes, including those hosting parasites, can invade the lower LCR from upriver sources >250 km away during freshets and provide a mechanism for the dispersal of invasive aquatic species in intermittent river systems.