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, 5× per week for 4 weeks in a swimming pool at 32-33 °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.