Background: The objectives of this review were to summarize systematic reviews with meta-analysis of balneotherapy (BT) and spa therapy (ST) based on randomized controlled trials, and to provide a perspective for future research. Methods: Eligible studies were systematic reviews based on randomized controlled trials with meta-analysis that included at least one group treated with BT or ST. We searched the following databases for articles published in English from the year 2000 to 20 November 2019: Cochrane Database Systematic Review, MEDLINE, CINAHL, Web of Science, and Ichushi-Web. Results: Eighteen studies met all inclusion criteria. Based on the International Classification of Diseases (ICD)-11, among these 18 studies, 8 (44%) were about "#15 Diseases of the musculoskeletal system or connective tissue", 5 (28%) were about "#21 Symptoms, signs or clinical findings, not elsewhere classified", 4 (22%) were about "#11 Diseases of the circulatory system", and 1 study (6%) was about "#8 Diseases of the nervous system". Both BT and ST provided significant pain relief and improved quality of life in chronic diseases of the musculoskeletal system and connective tissues. Additionally, BT and ST with exercise under water improved physical fitness and function in patients across diseases. Conclusion: Researchers need to conduct studies on the treatment of many kinds of potential diseases using the keywords of pain relief and QoL. In addition, depending on patients' symptoms, physical fitness, and disabilities, performing exercise under water may improve treatment effects on physical function and fitness.