Locomotor disorders involving the spine are a major cause of impaired performance and early retirement in sport horses. Swimming is increasingly incorporated into rehabilitation protocols, but its effects on spinal biomechanics remain poorly understood. This prospective study evaluated changes in thoracolumbar mobility in sixteen sport horses diagnosed with cervical or thoracolumbar axial musculoskeletal lesions over a 12-week rehabilitation program comprising 4 weeks of land-based training followed by 8 weeks during which swimming sessions were incorporated three times per week. Weekly measurements of thoracolumbar flexion–extension range of motion (ROM) were performed during straight-line trot on a hard surface using inertial measurement units attached to the withers, T18, and tubera sacrale. Group-level analyses revealed minimal changes across training phases: in horses with thoracolumbar lesions, mean ROM decreased slightly during the second month of aquatic training (−0.1° [95% CI −0.1; 0], Cohen’s d = 0.2), whereas no significant variation was detected in horses with cervical lesions. As the study did not include a control group, these temporal changes cannot be specifically attributed to swimming and should be interpreted as descriptive rather than causal. Individual trajectories showed heterogeneous patterns, but these were not consistent enough to alter the group-level interpretation. Overall, the findings suggest that thoracolumbar mobility remains relatively stable throughout this type of rehabilitation program, highlighting the importance of individualized monitoring rather than the expectation of a uniform biomechanical response.