[Purpose] The purpose of this study was to investigate the effects of balneotherapy on the cardiopulmonary function and physical capacity of pilots. [Subjects] Thirty-six healthy male pilots were recruited. [Methods] All subjects received entire-body immersion bath therapy in thermomineral water for 30 min a day for 21 days. Electrocardiograms, carotid pulse traces, and phonocardiograms were recorded using a cardiac function measuring device. Pulmonary function tests were performed using a Pony FX spirometer. The physical capacity of pilots was examined 1 day before and after balneotherapy. [Results] After 21 days of treatment, isovolumetric contraction time and the ratio of isovolumetric contraction time/left ventricular ejection time were reduced. Forced vital capacity, peak expiratory flow, the ratio of forced expiratory volume in 1 second/ forced expiratory volume and forced expiratory flow at 25–75% were elevated. The exercise numbers of pull-ups and sit-ups in 1 min were boosted. [Conclusion] The findings imply that balneotherapy for 21 days has a significant effect on the cardiopulmonary function and physical capacity of pilots.