Water pollution arising from abandoned coal mines, is second only to sewage as a source of freshwater pollution and in coalfield catchments mine water can be the dominant pollutant, with oxidised iron smothering the bed of receiving rivers. This study measured greenhouse gases in mine water outflows from sixteen sites across the Midland Valley in Scotland. Radiogenic and stable carbon isotopes measurements (Δ 14 C and δ 13 C) were used to determine the sources of both methane (CH 4 ) and carbon dioxide (CO 2 ) produced within the flooded mine environment. Concentrations of CH 4 -C ranged from 20 to 215 μg l -1 and CO 2 -C from 30 to 120 mg l -1 , with CO 2 accounting for 97 % of the mine water global warming potential. Methane origins included 51 % modern biogenic, 41 % thermogenic and 8 % from hydrogenotrophic methanogenesis of coal. The most significant inverse impact on biogenic CH 4 concentrations was sulphate, most likely due to sulphate reducing bacteria outcompeting methanogens. Carbon dioxide origins included 64 % from the dissolution of limestone, 21 % from terrestrial organic carbon and 15 % from coal. The limestone derived CO 2 was positively correlated with high sulphate concentrations, which resulted in sulphuric acid and caused the dissolution of carbonate from limestone. The mine waters experienced significant carbonate buffering becoming only slightly acidic (pH 6-7), but with significant loss of inorganic carbon. The mine waters had low dissolved oxygen (6-25 %) and high dissolved iron (2 to 65 mg l -1 ) and manganese (0.5 to 5 mg l -1 ) concentrations. Dissolved greenhouse gases from abandoned mines were estimated as 0.27 +0.31-0.18% of Scotland's global warming potential. This novel work has contributed information about the sources and controls of greenhouse gas fluxes in mine waters and identified the need to quantify and report this emissions term.