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We investigated how stream fragmentation affects local fish species persistence and extinction from three Rio Grande systems (Texas, USA) stream reaches with different levels of natural fragmentation. We examined species-volume (SV) relationships of fish assemblages in 42 pools across the watersheds and predicted greater fragmentation would correspond to an increase in the slope of the SV relationship due to decreased within-reach rescue effects. In addition, we examined relationships among tributary-specific nested subset patterns, local habitat features and spatial position of the reaches relative to the Rio Grande mainstem to better understand the importance of local and regional processes on fish species richness patterns in the stream reaches. Slopes of the SV curves did not differ among the stream reaches, but the intercepts of the SV curves were significantly different. These results indicated rescue effects among habitats within a stream reach were not apparent; however, rescue effects from the mainstem largely determined the species richness of a given stream reach. The nested subset patterns in all stream reaches were related to several local environmental factors, and large, deep pools provided important aquatic refugia in all three systems. We suggest declines in mainstem and tributary flows will likely continue to impact local and regional fish assemblage attributes. High flow events are important for dispersal and can reset tributary fish communities for the next extinction-driven, successional cycle.