The aim of this study was to investigate the effects of balneotherapy on chronic low back pain. This is a minimized, follow-up study evaluated according to the analysis of intention to treat. The subjects included in the study were 105 patients suffering from chronic low back pain. The control group (n = 53) received the traditional musculoskeletal pain killer treatment, while the target group (n = 52) attended thermal mineral water treatment for 3 weeks for 15 occasions on top of the usual musculoskeletal pain killer treatment. The following parameters were measured before, right after, and 9 weeks after the 3-week therapy: the level of low back pain in rest and the level during activity are tested using the Visual Analog Scale (VAS); specific questionnaire on the back pain (Oswestry); and a questionnaire on quality of life (EuroQual-5D). All of the investigated parameters improved significantly (p < 0.001) in the target group by the end of the treatment compared to the base period, and this improvement was persistent during the follow-up period. There were no significant changes in the measured parameters in the control group. Based on our results, balneotherapy might have favorable impact on the clinical parameters and quality of life of patients suffering from chronic low back pain.