A chemometric approach coupled with capillary electrophoresis based on the hierarchical cluster analysis and principal component analysis has been applied for the investigation of the water quality in the Golcuk-Isparta region (Lake District of Turkey). In the research area, Egirdir Lake, Golcuk Lake and surrounding ground and domestic waters have been utilized as drinking water resources. Golcuk Lake is distinctive in terms of high fluoride content (3.50 +/- 0.21 mg/mL) which is endemic in volcanic areas where the water flow through volcanic rocks and sediments. Based on the analysis of major anions chloride, sulfate, nitrate and fluoride with capillary electrophoresis, twenty-four drinking water sampling sites in the research area were classified into four classes using the hierarchical cluster and principal component analysis. Combining the research area investigation results of hierarchical cluster and principal component analysis, it was found that fluoride concentration is the major diagnostic variable to determine the quality of drinking waters, and all the other anions are the important classification factors to predict the resources of the drinking water samples, individually. To sum up, this study reveals the potential of the use of capillary electrophoresis in combination with chemometric techniques for the determination of the quality and origin of drinking waters.