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Intermittent headwater streams serve important functions for humans and wildlife in semi-arid rangelands. Increases in ashe juniper coverage in central Texas over recent decades are believed to have negatively impacted stream flows. Few studies have examined relationships between aquatic species and environmental factors in these systems as well as the influence of juniper coverage on assemblage structure. During summer 2003 and spring 2004, we examined species-environment relationships to infer potential effects of juniper cover on aquatic ecology relative to local-scale and watershed-scale environmental variables. Fish and crayfish species assemblages and physicochemical variables were investigated in spring-fed headwater tributaries of the Pedernales River, Texas. Fish abundance was much higher in summer 2003, whereas crayfish abundance was higher in spring 2004. Fish species richness was lower during spring 2004, possibly due to below average precipitation during spring 2004 that reduced deep-water refugia. Higher abundance of crayfish in spring 2004 samples was probably due to their ability to survive low-flow conditions, and a release from fish predation pressure. Fish assemblage structure was more strongly associated with local abiotic factors during spring 2004 when flow was reduced, whereas structure during summer 2003 samples suggested a relatively greater influence of predation. In general, juniper cover was weakly associated with fish and crayfish assemblages, although it tended to be positively associated with relatively high-quality habitat for sensitive taxa (flowing runs with coarse substrate; deep, connected pools). We suggest that intermediate levels of juniper cover in the region provide indirect benefits to aquatic organisms. However, short-term, local environmental factors appear to have a much greater influence than watershed vegetation on fish and crayfish assemblages in these intermittent streams. Copyright (C) 2007 John Wiley & Sons, Ltd.