Objective: To evaluate the effects of water and mat Pilates on pain, disability, and static and dynamic balance in patients with chronic nonspecific low back pain (CNLBP). Methods: Twenty-four participants with CNLBP were randomly allocated into two groups (n ¼ 12) that perform water and mat Pilates exercises for 24 sessions (8-week, 3 sessions per week). The value for pain, disability and balance were measured before and after the exercise program using the Visual Analogue Scale, Oswestry Disability Questionnaire and Biodex Balance System respectively. Results: A paired t-test revealed significant differences in pain severity and disability in both groups after they performed the Pilates program (P 0.05). Mat Pilates improved static balance as the participants performed the tests with their eyes open and closed (P ¼ 0.02, P ¼ 0.04). Its effect on dynamic balance, however, was not statistically significant (ES ¼ 0/33, P ¼ 0/34). The same Pilates program performed in water did not show significant effects on balance despite a decline in body sway (P˃0/05). There was no difference between the two groups (P˃0/05). Conclusion: The results suggest that both mat and water Pilates exercise program have beneficial effects on the treatment of LBP. Nevertheless, the low impact of the mat and water Pilates program on balance improvement suggests more investigation on Pilates training or complementary exercises to improve balance in patients with CNLBP.