Objective: Investigating the effect of 12 weeks of an aquatic exercise program on cardiac autonomic modulation by heart rate variability index of postmenopausal women with type 2 diabetes mellitus (T2DM). Methods: A randomized clinical trial was performed in 25 women aged 51 to 83 years, divided into exercise group (EG) (n = 13) submitted for 12 weeks to two weekly sessions of 50 minutes each, and control group (CG) (n = 12) without exercise. Results: Regarding cardiac autonomic modulation significant interaction was observed for TINN values (ms), indicating a slight increase in EG, but mostly a reduction in CG. The regression analysis also pointed effect of aquatic exercise on reducing the LF/HF ratio, after controlling for covariates diastolic blood pressure and dyslipidemia. Conclusion: The aquatic exercise had a significant effect on the reduction of cardiovascular risk, mainly in relation to glycemia and abdominal obesity, which may represent a protective effect of exercise in the progression of autonomic dysfunction, but its effect on autonomic modulation seems to depend on a greater volume and time with aquatic exercise.Keywords: diabetes, women, menopause, autonomic nervous system.