Salinity and geomorphology drive long-term changes to local and regional fish assemblage attributes in the lower Pecos River, Texas Christopher A. Cheek 1, *, Christopher M. Taylor 2 1 Department of Natural Resources Management, Texas Tech University, Lubbock, TX 79409, USA 2 Department of Biology, University of Texas-Pan American, Edinburg, TX 78539, USA Accepted for publication December 3, 2014 Abstract – 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 430 km 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. Key words: Pecos River; fish assemblage change; salinisation; spring flow; habitat loss Introduction Rivers and streams, particularly in arid regions, have been severely altered by humans via impoundment, water quality degradation, water diversion and exten- sive introduction of invasive species (Williams et al. 1985; Hubbs 1990; Fagan et al. 2002; Olden et al. 2006; Pool & Olden 2012). These alterations have led to decreases in aquatic biodiversity around the world (Dirzo & Raven 2003), including Texas where 44% of the native fishes are considered to be extinct, extirpated or imperiled (Hubbs et al. 2008). Like most rivers in the western United States, the Pecos River in West Texas has changed greatly since early accounts in the late 1800s. The first historical accounts suggest that the river ranged from 20 to 30 m wide with depths of 2–3 m and fast flow (Huser 2000; Hall 2002). Due to changes in flow regime, fragmentation, channelisation and irrigation, the Pecos River no longer attains its historical chan- nel dimensions or connectivity (Jensen et al. 2006). Besides decreases in water quantity, human activities have also impacted water quality through oil produc- tion and agricultural processes in the region. These practices have led to high levels of pesticides, heavy metals (Schmitt et al. 2004) and the primary water quality issue, high salinity levels (Miyamoto 1995; Hoagstrom 2003). Increased salinity along with altered habitat avail- ability has greatly influenced fish community struc- ture in the lower Pecos River resulting in a loss of native fish diversity (Linam & Kleinsasser 1996; Hoagstrom 2003). It is presumed that water quality and habitat in the Pecos River have continued to Correspondence: Christopher M. Taylor, Department of Biology, University of Texas-Pan American, Edinburg, TX 78539, USA. E-mail: Taylorcm@utpa.edu *Present address: Navajo Nation Department of Fish and Wildlife, P.O. Box 1480, Window Rock, AZ 86515, USA doi: 10.1111/eff.12214 1 Ecology of Freshwater Fish 2015 Ó 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd ECOLOGY OF FRESHWATER FISH