Exercise-related interventions have been recommended as one of the main components in the management of fibromyalgia syndrome (FMS). Water therapy, which combines water's physical properties and exercise benefits, has proven effective in improving the clinical symptoms of FMS, especially pain, considered the hallmark of this syndrome. However, to our knowledge, the mechanisms underlying water therapy effects on pain are still scarcely explored in the literature. Therefore, this narrative review aimed to present the current perspectives on water therapy and the physiological basis for the mechanisms supporting its use for pain management in patients with FMS. Furthermore, the effects of water therapy on the musculoskeletal, neuromuscular, cardiovascular, respiratory, and neuroendocrine systems and inflammation are also addressed. Taking into account the aspects reviewed herein, water therapy is recommended as a nonpharmacologic therapeutic approach in the management of FMS patients, improving pain, fatigue, and quality of life. Future studies should focus on clarifying whether mechanisms and long-lasting effects are superior to other types of nonpharmacological interventions, as well as the economic and societal impacts that this intervention may present.