Hydrotherapy has been utilized in horse rehabilitation programs for over four decades. However, a comprehensive description of the swimming cycle of horses is still lacking. One of the challenges in studying this motion is 3D underwater motion capture, which holds potential not only for understanding equine locomotion but also for enhancing human swimming performance. In this study, a marker-based system that combines underwater cameras and markers drawn on horses is developed. This system enables the reconstruction of the 3D motion of the front and hind limbs of six horses throughout an entire swimming cycle, with a total of twelve recordings. The procedures for pre- and post-processing the videos are described in detail, along with an assessment of the estimated error. This study estimates the reconstruction error on a checkerboard and computes an estimated error of less than 10 mm for segments of tens of centimeters and less than 1 degree for angles of tens of degrees. This study computes the 3D joint angles of the front limbs (shoulder, elbow, carpus, and front fetlock) and hind limbs (hip, stifle, tarsus, and hind fetlock) during a complete swimming cycle for the six horses. The ranges of motion observed are as follows: shoulder: 17 ± 3°; elbow: 76 ± 11°; carpus: 99 ± 10°; front fetlock: 68 ± 12°; hip: 39 ± 3°; stifle: 68 ± 7°; tarsus: 99 ± 6°; hind fetlock: 94 ± 8°. By comparing the joint angles during a swimming cycle to those observed during classical gaits, this study reveals a greater range of motion (ROM) for most joints during swimming, except for the front and hind fetlocks. This larger ROM is usually achieved through a larger maximal flexion angle (smaller minimal angle of the joints). Finally, the versatility of the system allows us to imagine applications outside the scope of horses, including other large animals and even humans.