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Flash floods in desert streams can be more sudden, brief, and severe compared to floods in mesic streams. To determine their biotic and abiotic effects, substrate composition, organic detritus abundance, and aquatic animal taxonomic richness and abundance were measured 8-16 d before and 7 d after a flash flood in a 122 m reach of a montane desert stream (Chihuahuan Desert, USA). The flash flood severely altered channel morphology by scouring and depositing substrates, but it did not change the overall abundance of any substrate particle size class. The flood removed most coarse detritus from the stream reach, although the quantity of organic particles <2 mm was unchanged. High losses were observed in most animal taxa (95 % overall), and reach-wide taxonomic richness was reduced from 35 to 21 taxa. Ephemeroptera were entirely eliminated from the study reach. The taxon experiencing the lowest percent loss (the belostomatid hemipteran Abedus herberti, 14 % loss) is known to possess behavioral mechanisms for flash flood avoidance. Compared to studies of flooding in mesic streams, this study suggests that flash floods in montane desert streams cause greater mortality in animal populations and remove more detritus. Ecologically, these high local mortality rates stress the importance of recolonization mechanisms. Evolutionarily, flash floods provide a strong selection pressure that may influence the genetic structure of populations.