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Chronic obstructive pulmonary disease promotes systemic repercussions, which can be minimized with physical exercise. This study investigated the effects of a water-based aerobic interval training program on the autonomic modulation of heart rate (HR), quality of life (QoL), and functional capacity (FC) of patients with chronic obstructive pulmonary disease.Nineteen patients with chronic obstructive pulmonary disease were enrolled in this randomized clinical trial and allocated to either the usual care group (n = 9) or training group (n = 10). Before and after 24 sessions of water-based physical training, the patients underwent evaluation of autonomic modulation of HR by analyzing the HR variability, QoL using the St George's Respiratory Questionnaire, and FC using 6-min walk test distance.The results showed significant improvement when comparing the variables of HR variability, QoL, and FC in the training group in the pre- and post-training conditions (P < .05). In the usual care group, there was no significant difference for any of the variables. Negative correlations were found between HR variability and QoL (r =−0. 55; P = .01) and 6-min walk test distance and QoL (r =−0.49; P = .02).Water-based physical training promoted beneficial adaptations in the autonomic modulation of HR, QoL, and FC of patients with chronic obstructive pulmonary disease.