Coal mining activity contributes to energy security and employment occupation, but is associated with environmental deterioration. Coal combustion leads to GHG emissions, while coal mining results in the generation of saline effluents. These effluents are discharged in inland surface waters, applying significant pressure on their quality, with a negative impact on aquatic life and the economy of a region. This study includes water samples that were analyzed in order to investigate the organic compounds, heavy metals, and other physicochemical parameters. Biological monitoring was done according to the Water Framework Directive methodology. The results from an aquatic area in Southern Poland, which indirectly receives coal mine effluents, indicate elevated salinity with excessive chlorides, sulfates, and sodium ions. The water quality of another non-polluted aquatic area was also assessed to examine the impact of indirect coal mine wastewater discharge on this area. The high salinity levels hinder the use of river water for drinking, agricultural, or industrial purposes. The results obtained show high pressure on the ecological status of streams and rivers that receive mine effluents, and on the density and diversity of aquatic invertebrates. This pressure is clearly visible in the structure of benthic communities and in invertebrate diversity. It also contributes to the appearance of invasive species and increasing water salinity. Limiting discharges of mine water transporting large loads of saline substances would reduce the negative impact on the quality of river waters and biological life.