Parasite assemblages acquired through trophic interactions in fish hosts are increasingly cited as a means to determine pollution effects on water quality and food web structure. We examined gastrointestinal parasite community changes above and below coal mine input from 597 individuals representing 3 species of sunfish: green sunfish (Lepomis cyanellus), bluegill (L. macrochirus), and longear sunfish (L. megalotis). Hosts were collected from 6 sites in or near the south fork of the Saline River Basin in southern Illinois in the spring and fall of 2006. Three sites received no known effluent from coal mines. An additional 3 sites received effluent termed acid mine drainage (AMD). We recovered 1,064 parasites from 12 genera. The parasite community in sunfish collected downstream nearest to the source of AMD was significantly different from 3 upstream sites. In addition, 2 sites farther downstream receiving AMD were different from 2 of 3 reference sites. However, there was also considerable variability in parasite assemblages between sites grouped as above or below coal mine effluent. Several parasite species responded to changes in water quality. Spinitectus sp. (Nematoda), which uses sensitive mayfly hosts to complete its life cycle, was less abundant at sites downstream of coal mine effluent in both green sunfish and bluegill. In contrast, 2 acanthocephalans (Neoechinorhynchus sp. and Eocollis arcanus) and a nematode (Spiroxys sp.) were found in green sunfish more frequently in areas downstream of AMD. This study further suggests metazoan parasites may be useful as indicators of water quality; however, variability among similar sites may limit their application. In addition, strong assemblage differences were found among the 3 sunfish species, suggesting variable habitat usage and potential resource partitioning among congeneric fish hosts in streams.