Fish communities at 10 sites in the Rio Grande Basin were sampled during low-flow periods between 1993 and 1995 as part of the U.S. Geological Survey National Water-Quality Assessment Program. The ecology of fish communities is one of several lines of evidence used to characterize water-quality conditions. This report describes the fish communities at selected sites in the Rio Grande Basin and relates the structure of these fish communities to the physical and chemical characteristics of the streams. Twenty-nine species of fish representing 10 families were identified in 25 samples collected during this study. Species richness ranged from 1 to 13. Cluster analysis of the 25 samples collected during this study delineated four groups of sites that were based on the similarity of the fish communities. The first two groups were individual sites with low species richness. The third group contained the most samples, and the fourth group consisted of samples from the Rio Grande at Isleta, New Mexico, and the Rio Grande at El Paso, Texas. The shift in community structure of samples from group 3 to group 4 reflects changes from predominantly coldwater fishes to warmwater fishes. Four metrics of biotic integrity (percentages of introduced individuals, omnivores, tolerant individuals, and anomalies) were used in this study to provide a broad overview of the community structure. The relative percentages of introduced species at the Rio Grande near Del Norte, Colorado; Saguache Creek near Saguache, Colorado; Rio Grande below Taos Junction Bridge, near Taos, New Mexico; and Rio Grande at Isleta are indicative of biological stress on the communities at these sites. The dominance of omnivores in samples from the Rio Grande below Taos Junction Bridge, near Taos; Rio Chama near Chamita, New Mexico; Rio Grande at Isleta; and Rio Grande at El Paso is an indication of environmental stress at these sites. In 1995, tolerant species accounted for the entire fish community at the Rio Grande at Isleta. In all samples the occurrence of anomalies was less than 2 percent of the individuals, with the exception of the sample from the Rio Grande at Isleta. On the basis of the relative percentages of introduced individuals, omnivores, tolerant individuals, and anomalies, the biotic integrity at the Rio Grande at Isleta appears to be the most impaired of all sites and shows indications of potential chemical and physical perturbations. Fish communities from three reaches at the Santa Fe River above Cochiti Lake, New Mexico, and the Rio Grande at Isleta were sampled in 1995 to assess small-scale spatial patterns in the structure of fish communities. The spatial pattern at these sites might be associated with natural variability of the fish communities or with the presence of habitat features such as pools. The total number of individuals and relative abundance in a sample varied at sites sampled yearly during this study. All sites, with the exception of the Rio Grande near Del Norte, had a decline in total number of individuals in a sample. The temporal decline in the total number of individuals at these site might be associated with the natural variability within the fish communities.