This study highlights the geochemistry of water and sediments of the karstic springs of the transboundary aquifer (TBA) Žumberak–Samoborsko Gorje Mt. (NW Croatia). After calculating pollution indices, the analysis showed that the sediments are unpolluted. The geo-accumulation index (Igeo) showed only the elements Ba and Rb, indicating moderate levels of pollution, with the highest values in springs Vapnik and Bistrac. Statistical analysis confirmed their natural origin. The water of these springs is under possible anthropogenic influence as indicated by elevated concentrations of total nitrogen (TN) and total phosphorus (TP). According to a principal component analysis (PCA) for elements in sediments, PC1 described a combined lithogenic and oxidative–reductive influence, PC2 described a combined geological background including total organic carbon (TOC) content and oxidative–reductive influence, while TOC had the greatest influence on PC3. Depending on element composition, the factor scores related to PC1 and PC2 resulted in two different groups of sites, while the factor scores concerning PC1 and PC3 did not show separation in two groups. The hierarchical cluster analysis showed three clusters in relation to the content of the elements. The correlation coefficient between the sediment and related water samples showed that the springs placed in a low-permeability formation (dolomite) had a strong positive coefficient of correlation.