Southern Kazakhstan is one of the fastest-growing regions of this country and continued development depends on a sustainable supply of freshwater for multiple purposes. Groundwater in Southern Kazakhstan occurs in a wide variety of hydrogeological conditions with varying levels of quality and vulnerability to contamination. The aim of this paper is to investigate the present groundwater quality through sampling and laboratory analysis of source water from public supply wells, compare results to hydrogeology and known contaminant sources, and indicate where future protections may be needed. Protection from surface-borne contaminants is mainly determined by the thickness of the vadose zone, depth of the groundwater level, presence, thickness and composition of aquifers, and mobility of pollutants. Forty-five wells were sampled, yielding 106 samples of groundwater presently used for drinking water, which were evaluated to investigate the occurrence of potential pollutants and hydrogeology of the region. Of the samples collected, 46 samples were used for analysis of inorganic water chemistry, 30 for individual indicators including metals, and 31 samples for determination of petroleum products. A contaminant inventory database and geospatial database aided the interpretation of the results and allowed the prediction of future water issues. Kazakhstan’s maximum permissible concentrations (MPCs) for metals were exceeded in areas associated with industrial enterprises, while fluoride and nitrate were more closely associated with mining and agricultural sources. Groundwater quality is dependent on hydrogeology and environmental contaminants resulting from historical land uses and must be regularly monitored for drinking water safety. Petroleum hydrocarbons were not detected in any of the drinking water sources.