We intensively sampled fishes from two reaches of the Rio Grande within the Albuquerque Basin (Albuquerque and Belen valleys) during 1998–2001, compared our findings with those from 1984, and compiled a list of all fishes known from the two reaches. Structure of assemblages (richness, diversity, abundance distributions–taxon dominance versus rank abundance) was similar between reaches in 1998–2001, but the faunas had low taxonomic similarity. The nonnative white sucker (Catostomus commersonii), western mosquitofish (Gambusia affinis), and native red shiner (Cyprinella lutrensis) dominated the Albuquerque Valley. Faunal change in the Albuquerque Valley between 1984 and 1998–2001 indicated all native fishes besides the red shiner declined, particularly the Rio Grande silvery minnow (Hybognathus amarus) and longnose dace (Rhinichthys cataractae). In contrast, the red shiner alone dominated the Belen Valley, nonnative fishes were less dominant, and aside from the Rio Grande silvery minnow and longnose dace, native species did not decline. Environmental differences provide a potential explanation for divergence of faunas between valleys, i.e., discharge in spring and summer is higher and substrate is coarser in the Albuquerque Valley. Dewatering, fragmentation by dams, and modifications of the river channel correspond to historical losses of fishes that require fluvial conditions. With the exception of the red shiner and, possibly, the fathead minnow (Pimephales promelas) and slender carpsucker (Carpiodes carpio), native fishes appear to be succumbing to combined stressors of change in habitat, intermittence of streamflow, and interactions with nonnative taxa.