A large number of treatments were used for patients with chronic low back pain. Frequent episodes have been reported very high. Although balneotherapy was found effective in this disease, there are not well-designed studies. We aimed to determine the effectiveness of balneotherapy versus physical therapy in patients with chronic low back pain. Exercise was added to both treatment programs. Sixty patients with chronic low back pain were randomly divided into two groups. Physical modalities plus exercise were applied to group 1, and group 2 was received balneotherapy plus exercise for ten sessions. The following parameters were measured: visual analogue scale at rest and movement for pain, paracetamol dose, manual muscle test for lumber muscles, modified Schoeber' test, Oswestry disability index, and Short-Form 36 at the beginning and end of the therapies and at the 3 months follow-up. The statistical analyses were performed using the SPSS 10.0 program. Both groups achieved significant improvements within themselves. But balneotherapy groups were improved at back extensor muscle test (P < 0.05), modified Schoeber's test (P < 0.03), Oswestry disability index, and the some scores of SF 36 (energy vitality, social function, role limitations related to physical problems, and general health P < 0.05). Balneotherapy combined with exercise therapy had advantages than therapy with physical modalities plus exercise in improving quality of life and flexibility of patients with chronic low back pain.