Anthropogenic alterations to lotic systems are often implicated in global declines among stream-dwelling fishes. A primary step toward mediating fish declines is improving our understanding of species—environment relationships; unfortunately, such information is limited. The goal of this study was to assess relationships between fish communities and environmental variables in a relatively intact portion of the Rio Grande/Rio Bravo del Norte in the southwestern United States and northern Mexico. We quantified the relationship between riverine habitats and local fish communities at 7 sites in the Big Bend reach of the Rio Grande/Rio Bravo del Norte during 2006. Monthly collections yielded 10,565 individuals representing 20 species, including 6 species listed as threatened or otherwise at risk. Species richness varied among sites (range 13–19) as did diversity (1 - D: 0.49–0.72) and density (16–45 fish · 100 m^-2). Fish community composition indicated spatial and temporal variations, but habitat characteristics indicated more variation among sampling sites than among months. Spatial variation in community structure correlated with site-specific habitat characteristics, and most threatened or at risk species were associated with run or riffle geomorphic units containing higher current velocities and gravel to cobble substrates. Temporal variation in community structure correlated with fall monsoonal flooding, during which composition of dominant species shifted from the habitat generalist red shiner (Cyprinella lutrensis) to the imperiled, regionally endemic Tamaulipas shiner (Notropis braytoni). Results from this study suggest that large flood pulses and maintenance of habitat heterogeneity are necessary for the persistence of both declining and intact local fish communities in the Rio Grande/Rio Bravo del Norte.