The effects of aquatic high-intensity interval training (AHIIT) on cardiometabolic and perceptive responses when compared to similar land-based exercise (LHIIT) remain unknown. Here, we aimed to (1) establish a matched intensity between mediums and (2) compare the acute cardiometabolic and perceptive responses to the two interventions in healthy young women. Twenty healthy young women performed a stationary running exercise at a matched exercise intensity. The incremental stages, in terms of percentage of heart rate (HR), maximal oxygen uptake (%VO2max), percentage of oxygen uptake reserve (%VO2R), percentage of heart rate reserve (%HRR), and rate of perceived exertion (RPE), were examined and acute cardiometabolic and perceptive responses were evaluated. The results showed that HR was significantly reduced (AHIIT: W 150 ± 19, R 140 ± 18, LHIIT: W 167 ± 16, R 158 ± 16 p < 0.01) and oxygen pulse (AHIIT: W 12 ± 2, R 10 ± 2, LHIIT: W 11 ± 2, R 9 ± 2 p < 0.05) was significantly increased with AHIIT compared to LHIIT. No significant group differences were observed for the perceptive responses. The comparable results demonstrated by the aquatic and land incremental tests allow precise AHIIT and LHIIT prescriptions. AHIIT had distinct differences in HR and oxygen pulse, despite having no distinct difference from LHIIT for some cardiometabolic and affective responses.