The objective of this study was to examine the possible natural sources of fluorides and boron in SilurianOrdovician (S-O) aquifer system, as the anomaly of these elements has been distinguished in groundwater of western Estonia. Water-rock interactions, such as dissolution and leaching of the host rock, are considered to be the main source of high fluoride and boron concentrations in groundwater. Altogether 91 rock samples were analysed to determine if high F -and B levels in groundwater could be attributed to certain aquifer forming rock types. Fluorine and boron contents in limestones and dolomites vary from 100 to 500 mg/kg and 5 to 20 mg/kg, reaching up to 1,000 and 150 mg/kg in marlstones, respectively. K-bentonites, altered volcanic ash beds, are rich in fluorine (400-4,500 mg/kg) and boron (50-1,000 mg/kg). Thus, clay-rich sediments, providing ion-exchange and adsorption sites for F -and B, are the probable sources of both elements in S-O aquifer system in western Estonia.