Background: The evidence of hydrotherapy after rotator cuff repair (RCR) is limited as most studies either used it as an adjuvant to standard land-based therapy, or have different initiation timing. This study aimed to compare hydrotherapy and land-based therapy with varying immobilization time. Methods: Patients who underwent RCR with a 10-days or 1-month immobilization duration (early or late rehabilitation) were prospectively randomized. Results: Constant scores significantly differed at three months only, with the best score exhibited by the late hydrotherapy group (70.3 ± 8.2) followed by late land-based (61.0 ± 5.7), early hydrotherapy (55.4 ± 12.8) and early land-based (54.6 ± 13.3) groups (p < 0.001). There was a significant interaction between rehabilitation type and immobilization duration (p = 0.004). The effect of hydrotherapy compared to land-based therapy was large at three months when initiated lately only (Cohen’s d, 1.3; 95%CI, 0.9–1.7). However, the relative risk (RR) of postoperative frozen shoulder or retear occurrence for late hydrotherapy was higher compared to early hydrotherapy (RR, 3.9; 95%CI, 0.5–30.0). Conclusions: Hydrotherapy was more efficient compared to land-based therapy at three months only and if initiated lately. Even though initiating hydrotherapy later brought greater constant scores at three months, it might increase the risk of frozen shoulders or retear compared to early hydrotherapy.