The Amargosa River Canyon of San Bernardino and Inyo County, California, has been designated by the Bureau of Land Management as an Area of Critical Environmental Concern, due in part to its unique flora and fauna. As a task of the Area of Critical Environmental Concern implementation plan, a survey of native fishes was conducted from June 21 to August 12, 2010. Geographic Information System tools were used to map sampling locations, which were spaced at 50-meter intervals. Global Positioning Systems were used to locate sampling stations, and stations with adequate water for successful trapping were sampled with baited minnow traps. Amargosa River pupfish (Cyprinodon nevadensis amargosae) and speckled dace (Rhinichthys osculus spp.) were widespread throughout Armargosa River Canyon. Throughout the study area 8,558 pupfish were captured at 194 stations; 3,472 speckled dace were captured at 210 stations; 238 red-swamp crayfish (Procambarus clarkia) were captured at 83 stations; and 1,095 western mosquitofish (Gambusia affinus) were captured at 110 stations. Pupfish were most abundant in open water habitat with native riparian vegetation, and they were significantly less abundant where the stream was completely covered by cattails or where saltcedar (Tamarix sp.) dominated the riparian corridor. There was no relationship between stream cover and speckled dace distribution. Non-native western mosquitofish and red-swamp crayfish densities were significantly higher in stream reaches dominated by saltcedar. The continued spread of saltcedar threatens to negatively affect pupfish and potentially reduce speckled dace abundance throughout the Amargosa River Canyon. This study can serve as baseline information for observing native fish populations in the future, as related to potential changes to the Amargosa River Canyon ecosystem.