OBJECTIVES: To evaluate the effects of a hydrotherapy programme on aerobic capacity and linear and non-linear dynamics of heart rate variability (HRV) in women with fibromyalgia syndrome (FMS). METHODS: 20 women with FMS and 20 healthy controls (HC) took part in the study. The FMS group was evaluated at baseline and after a 16-week hydrotherapy programme. All participants underwent cardiopulmonary exercise testing on a cycle ergometer and RR intervals recording in supine and standing positions. The HRV was analysed by linear and non-linear methods. The current level of pain, the tender points, the pressure pain threshold and the impact of FMS on quality of life were assessed. RESULTS: The FMS patients presented higher cardiac sympathetic modulation, lower vagal modulation and lower complexity of HRV in supine position than the HC. Only the HC decreased the complexity indices of HRV during orthostatic stimulus. After a 16-week hydrotherapy programme, the FMS patients increased aerobic capacity, decreased cardiac sympathetic modulation and increased vagal modulation and complexity dynamics of HRV in supine. The FMS patients also improved their cardiac autonomic adjustments to the orthostatic stimulus. Associations between improvements in non-linear dynamics of HRV and improvements in pain and in the impact of FMS on quality of life were found. CONCLUSIONS: A 16-week hydrotherapy programme proved to be effective in ameliorating symptoms, aerobic functional capacity and cardiac autonomic control in FMS patients. Improvements in the non-linear dynamics of HRV were related to improvements in pain and in the impact of FMS on quality of life.