The main aims of this study were to analyse the effect of a mineralized heated water inflow from a uranium ore processing plant on the abundance and diversity of epilithon and macroinvertebrate herbivores as well as to identify changes in functional feeding groups. In total, four sampling sites were selected. One site was on the mining water tributary and three sites in a recipient natural stream (the Nedveˇdicˇka River, Czech Republic): one of them upstream and two downstream from the mining effluent. Samples were taken monthly during the period 2008–2009. The number of species in the epilithon was higher downstream from the tributary and we also recorded a small increase in density. We observed significant changes in the taxonomical composition of epilithon and macroinvertebrate communities downstream from the tributary. Taxa richness of macroinvertebrates was similar between sampling sites. A small drop in macroinvertebrate abundance immediately downstream from the tributary was followed by a significantly elevated number of herbivores, especially scraper-collectors, at the more downstream site. Alteration of the species composition and abundance of herbivorous macroinvertebrates in the Nedveˇdicˇka River could be explained by a combination of a change in food availability and the physico-chemical properties of the water.