The geochemical and isotopic composition of surface waters and groundwater in the Velenje Basin, Slovenia, was investigated seasonally to determine the relationship between major aquifers and surface waters, water–rock reactions, relative ages of groundwater, and biogeochemical processes. Groundwater in the Triassic aquifer is dominated by HCO₃–, Ca²⁺, Mg²⁺and δ¹³CDICindicating degradation of soil organic matter and dissolution of carbonate minerals, similar to surface waters. In addition, groundwater in the Triassic aquifer has δ¹⁸O and δD values that plot near surface waters on the local and global meteoric water lines, and detectable tritium, likely reflecting recent (<50 years) recharge. In contrast, groundwater in the Pliocene aquifers is enriched in Mg²⁺, Na⁺, Ca²⁺, K⁺, and Si, and has high alkalinity and δ¹³CDICvalues, with low SO₄²–and NO₃–concentrations. These waters have likely been influenced by sulfate reduction and microbial methanogenesis associated with coal seams and dissolution of feldspars and Mg-rich clay minerals. Pliocene aquifer waters are also depleted in¹⁸O and²H, and have³H concentrations near the detection limit, suggesting these waters are older, had a different recharge source, and have not mixed extensively with groundwater in the Triassic aquifer.