This is a best-evidence synthesis providing an evidence-based summary on the effectiveness of aquatic exercises and balneotherapy in the treatment of musculoskeletal conditions. The most prevalent musculoskeletal conditions addressed in this review include: low back pain, osteoarthritis, fibromyalgia and rheumatoid arthritis. Over 30 years of research demonstrates that exercises in general, and specifically aquatic exercises, are beneficial for reducing pain and disability in many musculoskeletal conditions demonstrating small to moderate effect sizes ranging between 0.19 and 0.32. Balneotherapy might be beneficial, but the evidence is yet insufficient to make a definitive statement about its use. High-quality trials are needed on balneotherapy and aquatic exercises research especially in specific patient categories that might benefit most.