Abstract This study focuses on the characterisation and origin of hydrothermal waters discharging from three main active volcanoes (Furnas, Fogo and Sete Cidades) at São Miguel, where 33 water with temperatures ranging between 13 and 97 °C, and 5 precipitate samples were collected. The developed conceptual model for this active hydrothermal system reveals that all waters can be classified by Na-HCO3, Na-Cl and Na-SO4 types and are of meteoric origin. This is confirmed by the stable hydrogen and oxygen isotope data that are positioned close to the local meteoric water line (− 4.1‰ ≤ δ18OH2O ≤ 5.2‰; − 17.6‰ ≤ δDH2O ≤ 20.4‰), except for the Na-Cl type water at Ferraria (Sete Cidades area), which is characterized by admixing of seawater. The stable isotope composition of São Miguel hydrothermal solutions (δ34SSO4 range from 21.3 to − 3.7; δ18OSO4 range between 0.5 and 10.5‰; δ13CTDIC = − 4.5 ± 3.2‰) indicate that waters are individually evolved by several processes: evaporation, uptake of volcanogenic sulphur and carbon dioxide, leaching of local volcanic rocks (driven by high CO2 contents and/or elevated temperature), and biological activity. Latter hydrochemical superimposition is displayed by stromatolitic structures in the precipitates at the given site. Dissolved REE data show similar pattern as local volcanic rocks. In particular the distinct Eu anomaly hints to preferential leaching of locally occurring trachyte. The strongly acidic Na-SO4 waters sampled in boiling pools at Fogo and Furnas Lake indicate high leaching levels and LREE depletion versus HREE compared with the volcanic local rock compositions. Depletion in LREE is most likely caused by its preferential removal compared to HREE by the co-precipitation with alunite.