Information from research with animal models of immobilization and early motion following joint surgery drove human orthopedic surgeons to require physical therapy in their patients. This provided the basis for the physical therapy profession to be formed several decades ago. The same benefits of motion following joint surgery have not yet been explored in veterinary patients, as the first juvenile steps toward postoperative treatment have only been undertaken in the past few years. Few peer-reviewed manuscripts on rehabilitation in animals exist, and recommendations for the design and implementation of rehabilitation programs are nonexistent. This manuscript should serve as one of the first examples of how to establish a rehabilitation program for the dog. This is not an endpoint but rather the beginning. This serves to document the protocols and design of the Iowa State University, Veterinary Teaching Hospital, Canine Rehabilitation Center. This manuscript includes the design and implementation of this program, including but not limited to safety issues, water quality issues, patient care issues, and protocol recommendations. It also includes two of the first scientific reports submitted to peer-reviewed veterinary literature. The first, an evaluation of limb function comparing rehabilitation and traditional exercise-restriction after surgery for ruptured cranial cruciate ligaments, was accepted for publication by the Journal of the American Veterinary Medical Association. The other, a kinematic comparison of terrestrial and aquatic rehabilitation, has been submitted for publication. These scientific reports and this manuscript promote the use of aquatic rehabilitation for canine patients following a variety of orthopedic surgeries.