Six subterranean stream habitats in the central USA that contain rare and endangered cave animals were investigated. Water, sediment, and animal tissue were sampled to determine the degree of pollution inputs, and natural abundance stable carbon and nitrogen isotope analyses were employed to determine trophic structure and hypothetical influence of nutrient pollutants. Environmental quality sampling revealed contamination of water, sediments, and animal tissue by nutrients, toxic metals, and coliform bacteria, originating probably from septic systems and land application of animal feedlot wastes. Stable isotope analyses did not detect nutrient pollutants in the food webs of these habitats, but these analyses did elucidate trophic structure. Three trophic levels are evident in these subterranean streams: a detrital food base of clastic sediment, bat guano, and surface inputs; a second trophic level of detritivores, primarily crustaceans and amphibians; and a top level of predators, primarily fishes. Monitoring and management of sediment quality and flux is recommended to protect subterranean stream habitats.