Background. Inhalation of thermal water has been used empirically in the treatment of chronic diseases of upper and lower respiratory tract. This study investigates biomarkers of effect in exhaled breath (nitric oxide (NO)) and in exhaled breath condensate (EBC) (hydrogen peroxide (H 2 O 2 ), anions, toxic heavy metals of tobacco smoke) for patients with lung diseases inhaling salt-bromide-iodine thermal water. Methods. This study enrolled two groups of patients, twenty with alveolar pulmonary diseases—pneumoconiosis—twenty-two with bronchial diseases. Patients received 12 days inhalation treatment with thermal water in Terme of Monticelli (Parma), Italy. Results. No statistically significant differences were found for NO at different flow rates in both groups of patients before and after thermal water inhalation. Also in EBC no statistically significant differences were present for H 2 O 2 concentrations, toxic heavy metals concentrations, and anion concentrations before and after treatment. Nitrates in EBC were found to be significantly higher in patients before inhalation than in controls as well as in patients after inhalation versus controls. Conclusions. This study contributes to better quantify functional and biochemical changes in airways before and after thermal water treatment.