The fingerprinting concept that treats a chromatogram as a unique signal without peak identifying has been used in chromatographic comparative analysis. So far, no such approaches of ion chromatography have been published. Therefore, the aim of our work was to perform ion chromatographic analysis of five metals: Fe(III), Cu(II), Ni(II), Zn(II), and Mn(II) in 30 bottled mineral and spring waters available in the Polish market. The fingerprinting approach performed well and its main advantage is no need to perform the calibration procedure of each chromatographed ion. By investiging loadings, intercorrelated and orthogonal peaks were identified. We discuss the chemometric steps needed before comparison: smoothing, baseline removal, and warping.