Ankylosing spondylitis (AS) is a chronic systemic inflammatory disease that affects mainly the axial skeleton and causes significant pain and disability. Aquatic (water-based) exercise may have a beneficial effect in various musculoskeletal conditions. The aim of this study was to compare the effectiveness of aquatic exercise interventions with land-based exercises (home-based exercise) in the treatment of AS. Patients with AS were randomly assigned to receive either home-based exercise or aquatic exercise treatment protocol. Home-based exercise program was demonstrated by a physiotherapist on one occasion and then, exercise manual booklet was given to all patients in this group. Aquatic exercise program consisted of 20 sessions, 5x per week for 4 weeks in a swimming pool at 32-33 A degrees C. All the patients in both groups were assessed for pain, spinal mobility, disease activity, disability, and quality of life. Evaluations were performed before treatment (week 0) and after treatment (week 4 and week 12). The baseline and mean values of the percentage changes calculated for both groups were compared using independent sample t test. Paired t test was used for comparison of pre- and posttreatment values within groups. A total of 69 patients with AS were included in this study. We observed significant improvements for all parameters [pain score (VAS) visual analog scale, lumbar flexion/extension, modified Schober test, chest expansion, bath AS functional index, bath AS metrology index, bath AS disease activity index, and short form-36 (SF-36)] in both groups after treatment at week 4 and week 12 (p < 0.05). Comparison of the percentage changes of parameters both at week 4 and week 12 relative to pretreatment values showed that improvement in VAS (p < 0.001) and bodily pain (p < 0.001), general health (p < 0.001), vitality (p < 0.001), social functioning (p < 0.001), role limitations due to emotional problems (p < 0.001), and general mental health (p < 0.001) subparts of SF-36 were better in aquatic exercise group. It is concluded that a water-based exercises produced better improvement in pain score and quality of life of the patients with AS compared with home-based exercise.