Background: Obesity has been identified as a global epidemic that is associated with numerous comorbidities such as type 2 diabetes, hypertension, cancer, cardiovascular disease. We have investigated the effects of Watsu® therapy and Immersion on HRV parameters of obese male subjects. Methods and Results: Volunteer 34 obese subjects with BMI above 30 without any other chronic health issues were included (age, 18.30 ± 0.31, height, 166.02 ± 29.60, BMI, 36.54 ± 5.96). Randomized controlled trial was conducted with Watsu and Immersion protocols whereas control group received no therapy in water or on land for 12 weeks. A baseline HRV was recorded 5 minutes in four different circumstances. Polar H7 heart rate sensor and digital standardized HRV signal processing software were used to record the R-R intervals in millisecond. The repeated measures were used to compare the conditions between the therapies. The HRV analyses were performed using three-way Mixed ANOVA. Multiple comparisons were done with a Bonferroni adjustment of the alpha level (0.05). The collective results of HF showed significant negative effect (13.01 ± 1.36, 9.99 ± 1.11) and HF laying supine value (20.62 ± 2.22) was the highest (p<0.05). Conclusion: A significant inverse correlation was found between HRV values and both therapeutic interventions. Counterintuitively, 12-week of watsu and immersion therapies decreased LF and HF.