Vaalputs is the only South African nuclear waste disposal facility; it is licensed to dispose of low and intermediate level radioactive waste. Possible disposal of long-lived waste, potentially including spent fuel rods, prompted a study to establish a baseline of naturally-occurring radionuclides from the U and Th decay chains in the groundwater of Vaalputs. This baseline was created by investigating a dataset containing 25 years of analyses of the groundwater at the Vaalputs site. The behaviour over time, of 23 radionuclides in groundwater samples from 13 annually and three quarterly sampled boreholes, was evaluated and integrated in order to establish changing trends in the activities of radionuclides, the relative contributions of individual radionuclides to total radiation levels and how these were influenced by groundwater conditions. 238U levels showed a natural anomaly in the near-field of the disposal site that was attributed to the underlying basement rocks (granites) which are anomalously enriched in U. A set of duplicate samples from 2009 determined that the activity ratio of 234U/238U in the groundwater of Vaalputs is 4.1; this is ascribed to more rapid leaching of 234U relative to 238U, because of increased crystal structural damage around sites surrounding 234U atoms. High levels of 226Ra, unsupported by 238U, were found in groundwater from boreholes on the western side of the property: this groundwater yielded low values for 234U/238U, lower pH and stronger oxidizing conditions than groundwater from the rest of the area. The absence of overlying sedimentary rocks, which tend to ameliorate the effects of high radiation from granites by absorption, is suggested as the reason for the different geochemical conditions of the groundwater from boreholes in the west. This suggestion may apply to those boreholes elsewhere in Namaqualand with low published concentrations of 238U, but exceptionally high levels of α -and β-emitters. 232Th and its daughter radionuclides yielded radiation levels far below the guideline of 1 Bq.L-1 specified by the World Health Organization; this result is in line with the known low mobility of Th in groundwater systems.