Parasites and environmental conditions can have direct and indirect effects on individuals. We explore the relationship between salinity and parasites in an endemic New Mexico State threatened fish, the White Sands pupfish (Cyprinodon tularosa). Spatial variation in salinity limits the distribution of the endemic springsnail (Juturnia tularosae) within Salt Creek, a small desert stream. The springsnail is the presumed intermediate host for trematodes that infect the White Sands pupfish, and trematode prevalence and intensity in pupfish are positively associated with the springsnail. Salinity and parasites both have negative impacts on pupfish, but in areas of high salinity, pupfish can effectively escape parasites. Pupfish trematodes were absent from sites lacking snails. At the upstream site, the absence of parasites and lower variance in salinity were correlated with larger pupfish that were in better condition than pupfish at either the middle or lower sites. Springsnails were present in the middle section, an area with moderate salinity, and all pupfish had trematodes (median abundance 847 trematodes/fish). Lipid levels and condition were lowest in fish from the middle site. Additionally, fewer older fish indicated an increased mortality rate. At the lower site, springsnails were absent due to high salinity; pupfish trematode abundance was much lower (six trematodes/fish), and fish condition was intermediate. An additional experiment revealed that snail activity and survival were significantly reduced at high salinities commonly present at the lower site. Although both high salinity and parasites significantly affect pupfish, parasites might be more detrimental.