The geochemical and isotopic composition of groundwater in the Velenje Basin, Slovenia, was investigated between the years 2014 to 2015 to identify the geochemical processes in the major aquifers (Pliocene and Triassic) and the water–rock interactions. Thirty-eight samples of groundwater were taken from the aquifers, 19 in the mine and 19 from the surface. Groundwater in the Triassic aquifer is dominated by HCO3–, Ca2+ and Mg2+ with δ13C DIC values in the range from -19.3 to -2.8 ‰, indicating degradation of soil organic matter and dissolution of carbonate minerals. In contrast, groundwater in the Pliocene aquifers is enriched in Mg2+, Na+, Ca2+, K+, and Si, and has high alkalinity, with δ13CDIC values in the range of -14.4 to +4.6 ‰. Based on the δ13CDIC values in all the aquifers (Pliocene and Triassic), both processes inflence the dissolution of carbonate minerals and dissolution of organic matter and in the Pliocene aquifers, methanogenesis as well. Based on Principal Component Analysis (PCA), and on geochemical and isotopic data we conclude that the following types of groundwater in Velenje Basin are present: Triassic aquifers with higher pH and lower conductivity and chloride, Pliocene, Pliocene 1 and Pliocene 2 aquifers with lower pH and higher conductivity and chloride contents, and Pliocene 3 and Pliocene 2, 3 aquifers with the highest pH values and lowest conductivities and chloride contents. 87Sr/86Sr tracer was used for the fist time in Slovenia to determine geochemical processes (dissolution of silicate versus carbonate fraction) in Velenje Basin groundwater of different aquifers dewatering Pliocene and Triassic strata. 87Sr/86Sr values range from 0.70820 to 0.71056 in groundwater of Pliocene aquifers and from 0.70808 to 0.70910 in groundwater of the Triassic aquifer. This indicates that dissolution of the carbonate fraction prevails in both aquifers, while in Pliocene aquifers, an additional silicate weathering prevails with higher 87Sr/86Sr isotope ratios.