Cardiac rehabilitation (CR) plays a crucial role in managing patients who have undergone coronary intervention (CI) following acute myocardial infarction. While water-based exercise is gaining recognition as an exercise modality in this patient population, its impact on the subgroup of older adults remains unexplored. In this post hoc analysis, we investigated the effects of water-based exercise on adults older than 60 years undergoing CR after CI, comparing it to land-based exercise and a control group. In total, 45 patients aged over 60 participated in 14-day exercise programs, featuring two daily 30-min sessions. We assessed exercise capacity (VO2peak), vascular function (flow-mediated vasodilation (FMD)), heart rate variability (HRV), and blood markers (Interleukins 6, 8, and 10, P-Selectin, ICAM, and High-sensitivity CRP) before and after CR. VO2peak in the water-based group improved significantly after CR in comparison with the land-based group: 1.35 kg/mL/min (95% CI [0.20–2.50], p = 0.022). The significant difference between water-based and land-based groups was observed in several HRV parameters: Total power −1129.20 ms2 (95% CI [−1951.92–−306.49], p = 0.008); peak LF 0.04 Hz (95% CI [0.00–0.08], p = 0.036); SD1 −9.02 millisecond (95% CI [−16.86–−1.18], p = 0.025); and SD2 −19.71 ms (95% CI [−35.08–−4.34], p = 0.013). FMD and blood markers did not vary significantly based on the exercise group. These findings suggest that short-term water-based CR may have potential as an alternative to traditional land-based CR, improving VO2peak and cardiorespiratory fitness among adults over 60 years undergoing CR after CI.