The chemical composition of groundwater was studied and plausible reasons for its peculiarities were evaluated on the basis of long-term groundwater monitoring data. Fluoride and boron anomaly was distinguished in the Silurian-Ordovician aquifer system in western Estonia. The chemical type of groundwater controls the dissolution of fluorides and boron in water. Their concentrations are highest in deep groundwater having long residence time in the host rocks. The dissolution of carbonate rocks and clayey K-bentonite beds are the sources of F in groundwater. Barium anomaly in the Cambrian-Vendian aquifer system occurs in northeastern Estonia, where the intrusion of saline groundwater from the weathered crystalline basement contributes to the formation of Ba-rich groundwater. The overexploitation of fresh groundwater has resulted in the increase in groundwater salinity, however, detectable intrusion of seawater into the Cambrian-Vendian aquifer system is ruled out by the stable isotope signature.