Background and objectives: Aquatic exercises have demonstrated several advantages over land-based exercise, but only a few studies have compared the workout intensities and efficiencies in a stage-specific manner. This study aimed to investigate workout intensity during aquatic and land-based running, based on the rating of perceived exertion (RPE). Materials and Methods: Twenty healthy young male subjects underwent a land-based running test (LRT) and an aquatic running test (ART), in the form of a cardiopulmonary exercise treadmill test and a shallow-water running test. The seven stages of the ART were composed of 3 minutes each of the Bruce protocol performed during the LRT. In the ART, the participants were instructed to run in a swimming pool with matching RPE to that obtained at each stage of the LRT. Results: Heart rate (HR) during both LRT and ART exhibited a linear relationship (r = 0.997 and 0.996, respectively; p < 0.001). During the initial and middle period, HR was higher in the ART than in the LRT. However, in the final period, HR was higher in the LRT than in the ART. Conclusions: In aquatic exercises based on the RPE obtained from the LRT, HR exhibited a linear relationship in both the ART and the LRT. The ART appears to increase cardiac loading more efficiently in the initial period and does not increase cardiac loading abruptly at a later period. Although there is no precise, objective, controlled parameter to compare the ART and the LRT, the RPE may be used as a convenient measurement for workout intensity in aquatic running.