Intermittent headwater streams serve important functions in semi-arid rangelands, both for humans and wildlife. However, few studies have assessed species-environment relationships for fish and benthic macroinvertebrate assemblages in these systems. Additionally, no published studies could be found that addressed the influence of juniper coverage in watersheds on assemblage structure of these taxa. Increased juniper coverage in recent decades is believed to be associated with decreased water yields in central Texas streams. During summer 2003 and spring 2004, I examined potential effects of juniper cover on aquatic ecology. Fishes, benthic macroinvertebrates, and the physicochemical habitat were investigated in spring-fed headwater tributaries of the Pedernales River. My objectives were to: 1) describe the typical fish and benthic macroinvertebrate assemblages in headwater creeks of the Pedernales River basin; 2) compare seasonal variability of fish and benthic macroinvertebrate assemblages; 3) identify species-environment relationships in this river basin; and 4) evaluate the influence of juniper coverage in the watershed, relative tolocal and landscape-level environmental factors, on the structure of fish and benthic macroinvertebrate assemblages. A total of 4,181 individual fish were collected in summer 2003 samples, 551 fish were collected in spring 2004, 59,555 macroinvertebrates were captured in summer 2003 samples, and 51,500 macroinvertebrates were collected in spring 2004. Assemblages were typical for the area and habitat conditions. Faunal richness was lower in spring than in summer, possibly due to a combination of sampling after a relatively dry period in the spring, and lack of winter refugia in the form of deep pools. Fish assemblages may structure based principally on abiotic factors in spring, the harsher season (less available water), whereas predation pressure may influence structure in summer. Another important environmental gradient for both fish and invertebrate assemblages contrasts pool and run mesohabitats. In general, juniper cover was weakly associated with fish and invertebrate assemblages, although it tended to be associated with relatively high quality habitat for sensitive taxa (flowing runs with coarse substrate; deep, connected pools). In these intermittent streams, local-scale environmental factors probably are the dominant influences on fish and benthic macroinvertebrate assemblages. Implications for future studies are discussed.