This study investigated the mineralogical and isotopic composition of groundwater and precipitation to identify and constrain geochemical processes within stacked Pliocene and Triassic aquifers in the Velenje coal basin. Scanning electron microscopy combined with energy-dispersive X-ray spectroscopic analysis revealed that suspended matter in the Pliocene aquifer consists of feldspars and quartz, while dolomite, calcite and feldspars are present in the aquifer dewatering Triassic strata. The concentrations of trace elements in Triassic and Pliocene aquifers range from highest to lowest Zn > Fe > Ni > Al > Ba > Mn > B>Li > Mo > As with the majority of trace element concentrations below international drinking water health guidelines. Multivariate principal component analysis indicated that concentrations of Mn, Ba, Eu, Cs, Y, Li and T, pH, conductivity and dissolved oxygen in samples were the best chemical parameter for distinguishing the two aquifers. A significant positive correlation (p < 0.05) was found between Ni, Mn, Co, Zn, As and Mo. Groundwater in the Pliocene aquifer likely has an external source of carbon based on the δ13CCO2 values (− 12.3 to − 3.6‰). The groundwater also has detectable levels of dissolved methane with isotopic values (− 77.7 to − 51.4‰ δ13CCH4; − 247 to − 162‰ δ2HCH4) consistent with microbial methanogenesis. The groundwater in the Triassic aquifer has tritium values (up to 4.1 TU 3H) characteristic of modern recharge (< 50 years), while the lack of detectable 3H (0 TU) in the Pliocene aquifer is consistent with longer residence times.