The assessment of the environmental quality of a sensitive karst aquatic system under the centuries-long anthropogenic influence of the coal mining industry is important for both improving the quality of water resources and protecting aquatic wildlife and human health. In this study, we investigated the anthropogenic impact on the aquatic environment of the upper and middle course of the Raša River through the analysis of a suite of metal(loid)s in three aquatic compartments (water, sediment, fish) using inductively coupled plasma mass spectrometry (ICP-MS). Concentrations of inorganic constituents in water were low, while the chemical composition of stream sediments mainly reflected the geological background of the area, indicating the origin of metal(loid)s from predominantly natural sources. Although comparison with PEC-Q values indicated that existing sediment quality conditions could pose a threat to benthic organisms with regard to Cr and Ni, the constant vertical profiles of these elements suggested their natural origin from the weathering of flysch. Element levels in the muscle of targeted fish species were in accordance with the values typical for low-contaminated freshwater systems, while levels of Cd, Pb and Hg were mostly below the European regulatory limits for toxic elements in foods, indicating that the low concentrations of most contaminants in muscles of fish from the Raša River do not present a risk to humans or other consumers. The obtained data indicated a generally low contamination status of the western part of the Raša River basin with regard to the analyzed inorganic elements.