During 2003–04 the U.S. Geological Survey, in cooperation with the National Park Service, re-evaluated the status of fish communities in three reaches of the Rio Grande in Big Bend National Park that originally were evaluated when the three reaches were established for study in 1999. The objective was to determine whether there were measurable differences between 1999 and 2003–04 (referred to as 2004) fish community status that likely are attributable to a rare 58-day period of low flow (less than 1 cubic meter per second) in spring 2003 at the Johnson Ranch gaging station on the Rio Grande in Big Bend National Park. The total number of fish species collected at all three sites (Boquillas, Johnson Ranch, and Santa Elena) in 1999 was greater than in 2004. The number of fish species collected at the Boquillas site in 1999 (10) was twice that collected in 2004; the number of species collected at the Johnson Ranch site in 1999 (nine) was almost twice that collected in 2004 (five). In contrast, the numbers at the Santa Elena site were nearly the same, 15 species in 1999, 14 in 2004. Percent community similarity for the Boquillas site is 8.04, for the Johnson Ranch site, 6.65, and for the Santa Elena site, 47.6, which indicates considerably more similarity between the 1999 and 2004 fish communities at the Santa Elena site than for the Boquillas and Johnson Ranch sites. At the Boquillas and Johnson Ranch sites, the fish communities shifted from small minnow (Cyprinidae) dominated in 1999 to largely gar (Lepisosteidae) and catfish (Ictaluridae) dominated in 2004. In contrast, no such shift occurred at the Santa Elena site between 1999 and 2004. Differences in flow conditions between the two downstream sites and the Santa Elena site might account for the dissimilar findings. The findings of the study provide some evidence that the spring 2003 period of low flow affected fish communities, but the findings are not definitive as other factors such as increased salinity, algal toxins, bioavailable contaminants, and exotic species can affect fish populations and, ultimately, fish community structure.