Silurian-Ordovician (S-O) aquifer system is an important drinking water source of central and western Estonia. The fluoride and boron contents of groundwater in aquifer system vary considerably. The fluoride concentration in 60 collected groundwater samples ranged from 0.1 to 6.1 mg/l with a mean of 1.95 mg/l in the study area. Boron content in groundwater varied from 0.05 mg/l to 2.1 mg/l with a mean value of 0.66 mg/l. Considering the requirements of EU Directive 98/83/EC and the Estonian requirements for drinking water quality, the limit value for fluoride (1.5 mg/l) and for boron (1.0 mg/l) is exceeded in 47 and 28 % of wells, respectively. Groundwater with high fluoride and boron concentrations is found mainly in western Estonia and deeper portion of aquifer system, where groundwater chemical type is HCO3-Cl-Na-Mg-Ca, water is alkaline, and its Ca(2+) content is low. Groundwater of the study area is undersaturated with respect to fluorite and near to equilibrium phase with respect to calcite. The comparison of TDS versus Na/(Na + Ca) and Cl/(Cl + HCO3) points to the dominance of rock weathering as the main process, which promotes the availability of fluoride and boron in the groundwater. The geological sources of B in S-O aquifer system have not been studied so far, but the dissolution of fluorides from carbonate rocks (F = 100-400 mg/kg) and K-bentonites (F = 2,800-4,500 mg/kg) contributes to the formation of F-rich groundwater.