Background <p>Chronic low back pain (CLBP) is a common musculoskeletal symptom associated with spinal disorders, impairing quality of life while imposing significant medical and socioeconomic burdens. Traditional land-based rehabilitation training is often limited by pain, whereas aquatic exercise utilizes water’s buoyancy, hydrostatic pressure, and viscosity to reduce spinal loading and provide a stable environment. Hot spring bathing employs thermal stimulation to dilate local blood vessels, enhance blood circulation in muscles and soft tissues, and alleviate muscle spasms and pain sensitivity. This study aims to evaluate the effects of combining hot spring bathing with aquatic exercise alongside conventional physical therapy on clinical symptoms and functional outcomes in CLBP patients.</p> Methods <p>A randomized controlled clinical trial was conducted with blinding of outcome assessors; participants were not masked to the intervention group, in which 36 participants were randomly distributed into control and intervention groups. The control group received conventional physical therapy, while the intervention group additionally underwent aquatic exercise combined with hot spring bathing. The primary (subjective pain intensity, degree of functional impairment) and secondary outcomes (motor Balance Ability, lower back muscle strength) were evaluated before and after the session using the Visual Analogue Scale (VAS), Oswestry Disability Index (ODI), Functional Movement Screen scale (FMS), and BCS-400 electronic back dynamometer. For all outcomes, multiple mixed 2 (group) × 2 (time) ANOVAs were performed.</p> Results <p>After intervention, the outcome measures of VAS, ODI, FMS and back muscle strength were improved significantly in intervention groups. There was a significant difference in the VAS change in the control group, while no significant differences were observed in ODI, FMS, or lumbar back muscle strength. It was noteworthy that the intervention group showed greater improvement after intervention than the control group: △VAS: 2.56 ± 0.92 &amp; 0.94 ± 0.54; △ODI: 9% ± 6% &amp; 4% ± 5%; △FMS: 3.44 ± 2.20 &amp; 1.44 ± 1.62; △back muscle strength: 18.50 ± 8.52 &amp; 12.44 ± 7.69&#xa0;kg, all the changes showed significant difference between two groups.</p> Conclusions <p>Aquatic exercise combined with hot spring bathing can significantly enhance the therapeutic effect of conventional physical therapy in CLBP patients, alleviating the subjective pain intensity and functional impairment, and improving motor function and lumbar and back strength.</p> Trial registration <p>This study has been prospectively registered with the China Clinical Trial Registry (ChiCTR) (Registration Number: ChiCTR2500106741/29. 07. 2025, <a href="https://www.chictr.org.cn/bin/project/edit?pid=280890">https://www.chictr.org.cn/bin/project/edit?pid=280890</a>) and was conducted in the hydrotherapy department of a specialized rehabilitation center.</p>