Background: Nowadays, low back pain (LBP) is one of the common musculoskeletal disorders. In addition to suffering from general pain, people with LBP encounter with limited mobility, functional disability and failure to balance maintenance in physical activities. With regard to different treatment methods for LBP, the present study has analyzed the effects of water and land Pilates on female patient with Chronic Nonspecific LBP (CNLBP). Materials and methods: The study was performed on 24 participants with CNLBP. Participants were randomly divided into two groups each consisting of 12 members and were asked to perform water or land Pilates exercises for 24 sessions. The degrees of balance, pain, and disability were measured before and after the exercise using the Biodex balance system, the visual analogue scale, and the Oswestry disability questionnaire. Results: Significant decrease in pain severity and disability indices were seen in both groups after the Pilates exercises (p≤ 0. 05), but no difference were found between the two groups. Land Pilates also improved static balance in patients (p=0. 02), its effect on dynamic balance, however, was not statistically significant. The same exercises in water did not show significant effects on balance despite a decline in body sway. Conclusion: The land and water Pilates exercises were useful for the treatment of LBP; however, this treatment strategy can be implemented in accordance with patient preference. Nevertheless, the low impact of the exercise on balance improvement suggests for complementary exercises for patients with CNLBP.