Abandoned mines cause serious environmental damage to surroundings, with considerable impacts on freshwater ecosystems. Impacts occur through uncontrolled discharge of polluted effluents containing contaminants with high salts concentrations. Currently, no real solution exists for this environmental problem, being a global pollution problem. This study evaluates the efficiency of an innovative treatment, proposed on Life DEMINE project, based on membrane processes, electrocoagulation and the combination of both, to decrease environmental impacts caused by mining effluents from abandoned mines on freshwater ecosystems, using aquatic biofilms as indicator of ecological impacts. We incubated natural biofilms from a reference stream in different microcosms under controlled temperature and light conditions. After two weeks of colonization, on cleaned and previously autoclaved cobbles, biofilms were exposed to treated and untreated effluents from Menteroda salt mine (Germany), mimicking the real dilution occurring when discharge into the aquatic ecosystems. Biofilms responses were measured at 1, 7 and 15 days after the exposure began. We observed a significant reduction of biofilm photosynthetic efficiency after 24h of exposure in all treatments that recovered one week later. Chlorophyll-a concentrations, diatoms and cyanobacteria community of aquatic biofilm were affected by all treatments compared to the control from 24h until the end of the exposure. Phosphate uptake capacity decreased significantly after 24h of exposure in all treatments but recovered one week later. These observations evidenced ecological impact of hypersaline mining effluents on aquatic ecosystems and the potential of the innovative treatment proposed to improve the quality of water bodies affected by abandoned mines.