In order to satisfy the needs of constant economic growth, the pressure to exploit natural resources has increased. Since accessible mineral resources are becoming scarce, the mining industry is constantly looking for novel techniques to allow commercial exploitation of lower-grade deposits. However, mining can have considerable impacts on freshwater ecosystems. Here, we present the ecological damage inflicted by mine water originating from the massive Terrafame Talvivaara polymetal mine (central Finland), where bioheap leaching is being applied to high-sulphur low-grade ore. We found that saline mine water has turned the lake meromictic, and sediment is heavily contaminated. As a result, important zooplankton and phytoplankton groups have been significantly altered. As the exploitation of poor-grade deposits is the future of the mining industry globally, water management should be taken to a higher level in order to proceed towards a sustainable mining sector.