Summary A study on the upper reaches of the Cecina River (Tuscany–Central Italy) and the associated unconfined aquifer was carried out from September 2007 to August 2008. The study aimed to identify the sources of B and As contamination in stream water and groundwater, and record contamination levels. The study area, which comprises a northern sector of the Larderello geothermal field, has in time been contaminated by both surface geothermal manifestations (now thought to have ceased) and anthropogenic activity. The latter refers to the disposal of spent geothermal fluids and borogypsum sludge, by-product of colemanite treatment with sulphuric acid, which until the late ‘70s were discharged in the Larderello area into the Possera Creek, a southern tributary of the Cecina River. A network of 22 stream sections and 9 observation wells was defined. Stream discharge (16 sites), well water levels and chemical concentrations (mainly B, As and anions) in water were measured monthly. Together, discharge and chemical concentrations were used to define the source of contamination by calculating the contaminant load in successive sections of the river network. Due to the stream’s intermittent flow, only 50% of the performed monthly surveys could be used in comparing the contaminant load at different sections. Both contaminant loads (referring to median to high flow conditions) and chemical concentrations suggest that B mainly derives from the leakage of a concentrated Na–SO4 water rich in B, SO4, NO3 likely from a small aquitard located in the Larderello area. The B load from this area is about 2 kg/h and increases to approximately 2.7 kg/h in the final section of the study area, likely due to contribution of groundwater. As mainly derives from dissolution and adsorption–desorption processes involving water and As-rich stream bed sediments. Of the total 15 g/h As load measured at the end section, only about 3 g/h derive from the Larderello area. Further to stream bed, As-rich sediments are also found at shallow depths in the area of the Cecina–Possera confluence and in the upper part of the aquifer skeleton. These sediments contribute to increase up to about 76 μg/L the As content of groundwater of the Cecina–Possera confluence area which, draining water from the Possera Creek, represents the aquifer root zone. This zone determines the B and As contents of groundwater which flows more or less parallel to the Cecina River, undergoes progressive dilution during its westward flow and locally supplies the same river. Most of the study stream water and groundwater in the study area cannot be exploited because mean B and As contents (respectively in the range 1.2–15.6 mg/L and 1.1–75.9 μg/L), are often well above the permissible limits for drinking water (1 mg/L for B, 10 μg/L for As).