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River systems throughout arid regions worldwide have been heavily impacted by human activities, resulting in long-term ecological consequences. The lower Pecos River in the Trans-Pecos region of Texas is no exception, having undergone anthropogenic changes that include decreased flow, elevated salinity, species loss and species invasion. We compared historical and contemporary fish assemblage attributes from the Pecos River at local (site-specific) and regional (Trans-Pecos region) scales across a 24-year time period. Fish assemblage data were collected in October 1987 and 2011, by seining at 15 sites spanning 430km of the river in Texas. Additionally, we examined contemporary environmental conditions to determine species-environment relationships. We found that fish assemblages were significantly different between time periods, likely due to increased salinisation in the upper half of the study region. Decreased species richness, species replacement and increases in euryhaline species were documented in the upstream sites. Freshwater springs lower the salinity and maintain flows in the downstream reach, allowing for maintenance of the native fish fauna. Careful management of regional aquifers, irrigation practices and petroleum waste water will be necessary for protecting biodiversity and environmental flows in the lower Pecos River.