Background and Objectives Obesity is one of the chronic diseases that is associated with metabolic disorders such as dyslipidemia. This study aims to determine the effect of a Aerobic Aquatic Trainingon body mass index (BMI), lipid profile, and atherogenic factors in middle-aged obese women. Subjects and Methods In the present quasi-experimental study, 30 middle-aged women with a BMI greater than 30 kg/m2 were randomly divided into two groups of exercise and control. Exercise program included six weeks of water aerobics at an intensity of 50-65% of the maximum heart rate (two sessions per week). Assessments were done during fasting 48 hours before and 48 after the exercise. Dependent t-test and analysis of covariance were used for statistical analysis. Results After the exercise period, a significant decrease in triglyceride (P=0.018) and the ratios of LDL to HDL (P<0.001) and total cholesterol to HDL (P<0.001) was reported as well as a significant increase in HDL, compared to the control group. However, no significant difference was observed in BMI (P=0.098), total cholesterol (P=0.318), and LDL (P=0.634). Conclusion Six weeks of water aerobics can improve lipid profile and reduces atherogenic factors in obese women without a significant effect on BMI.