The aim of this study was to investigate the efficacy of aquatic exercises in fibromyalgia syndrome (FMS). A total of 63 patients were included and allocated to two groups. Group I (n = 33) received an aquatic exercise program and Group II (n = 30) received a home-based exercise program for 60 min, 3x a week, over 5 weeks. Patients were evaluated for pain (visual analogue scale, VAS), number of tender points (NTP), Beck depression inventory (BDI), and functional capacity (fibromyalgia impact questionnaire, FIQ). All assessment parameters were measured at baseline, and at weeks 4, 12, and 24. There were statistically significant differences in FIQ and NTP in both groups at the end and during follow-up (P < 0.05). Group I showed a statistically significant decrease in BDI scores after 4 and 12 weeks (P < 0.05) that remained after 24 weeks (P < 0.001). In Group II, a significant decrease in BDI scores was observed at the end and during follow-up (P < 0.001). Also, a significant improvement was found in VAS at weeks 4 and 12 in both groups (P < 0.001). The average of reduction in pain scores was 40% in Group1 and 21% in Group II. However, this was still significant at week 24 only in the aquatic therapy group. A comparison of the two groups showed no statistically significant difference for FIQ, NTP, and BDI scores except VAS (P < 0.001) Our results showed that both aquatic therapy and home-based exercise programs have beneficial effects on FIQ, BDI, and NTP. In pain management, only aquatic therapy seems to have long-term effects.