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Background Knee joint dysfunction, including osteoarthritis, ligament injury, and post-surgical conditions, impairs symptoms, physical function, and quality of life. Aquatic rehabilitation leverages water’s buoyancy, resistance, and hydrostatic properties to reduce joint load and facilitate exercise, but evidence on its effectiveness across populations and intervention parameters is inconsistent. Methods We conducted a PRISMA-guided meta-analysis of randomized controlled trials (PROSPERO CRD420251139080) comparing structured aquatic exercise with land-based exercise or conventional treatment. Web of Science, PubMed, Embase, SPORTDiscus, CINAHL, and Cochrane Library were searched to July 2025. Change-score standardized mean differences (SMDs) with 95% confidence intervals (CIs) were pooled using random-effects models across symptoms, physical function, and quality of life. Heterogeneity was assessed using the I 2 statistic. Pre-specified subgroup analyses examined disease type, age, session length, intervention duration, and training frequency. Risk of bias was assessed with RoB 2.0; evidence certainty was appraised using GRADE. Results Twenty-nine trials (n = 1,984) were included. Aquatic rehabilitation significantly improved symptoms (SMD = −0.55, 95% CI: −0.73 to −0.38) and physical function (SMD = 0.50, 95% CI: 0.34 to 0.65) versus controls, while quality of life improvements were non-significant (SMD = 0.17, 95% CI: −0.15 to 0.50). Benefits were largest in patients with knee osteoarthritis and those <60 years. Interventions ≥8 weeks yielded greater symptom and functional gains. Functional subdomain analysis revealed pronounced improvements in balance, proprioception, and muscle strength, whereas mobility and flexibility showed smaller effects. Session length and training frequency had a minor influence. QoL improvements were primarily observed in younger participants. Conclusion Aquatic rehabilitation effectively alleviates symptoms and enhances physical function in individuals with knee joint dysfunction, with the greatest benefits observed in knee osteoarthritis patients and adults younger than 60 years. Programs lasting at least 8 weeks yield optimal outcomes, particularly for balance, proprioception, and muscle strength. While improvements in quality of life are less consistent, younger participants may experience psychosocial gains. These findings support the integration of structured aquatic exercise into knee rehabilitation protocols, with attention to patient characteristics and program duration to maximize therapeutic effects. Systematic review registration https://www.crd.york.ac.uk/PROSPERO/view/CRD420251139080 , identifier CRD420251139080.