Partizansk Coal Basin, located in the south of the Russian Far Eastern Region, was intensively mined from 1918 until 1998. Although it was mostly explored by underground excavation, the natural landscapes were transformed into anthropogenic ones. After the mines closed, ground subsidence occurred widely, especially in areas near the waste dumps. This caused water tables to rise to the surface and pollute the soil. Analysis of the hydrochemical composition of the mine waters were conducted in 2011–2013, and showed low alkalinity and average level of mineralization. This can be explained by the fact that while going up through soil mass, the mine waters lost their much of their pollutants due to soil buffering. All mine water samples contain thermo-tolerant coliform bacteria E. coli that indicates a source of fresh fecal pollution. Our research indicates increased hydrocarbon ion concentrations in mine waters, especially in autumn, that resulted in accumulation of chromium and copper compounds, which can cause soil pollution. A strong relationship between the chemical composition of the mine waters and soil extracts was found within areas of unregulated groundwater discharge on the surface. Significant negative correlation between pH and content of metal compounds including chromium and copper was found at the “Avangard” mine (r = − 0.95); and between alkalinity and chromium content at the “Glubokaya” mine (r = − 0.94). © 2019 International Research and Training Center on Erosion and Sedimentation and China Water and Power Press.