We investigated the effects of 8-week aquatic moderate-intensity continuous training (aMICT) and aquatic high-intensity interval training (aHIIT) on body composition, aerobic fitness, arterial stiffness, and endothelial function in overweight and obese young adults (OOYA). Sixty-one OOYA were randomly assigned to aHIIT, aMICT, or Control group. aHIIT group underwent twelve 30-second exercise bouts with the intensity of 85-95% HRmax, with a 60-second rest between each bout. aMICT group underwent an uninterrupted exercise with the intensity of 70-75% HRmax for 30 minutes. Endothelial function was assessed using brachial artery flow-mediated dilation (FMD) and arterial stiffness was evaluated through pulse wave velocity (PWV) and ankle-brachial index (ABI). Results revealed that aHIIT but not aMICT decreased ABI and increased FMD and skeletal muscle mass, whereas only aMICT decreased resting heart rate. A positive correlation was found between the change in weight with the change in FMD (r = 0.527, p = 0.020) after aHIIT. Following subgroup analysis, a positive correlation between change in weight and change in FMD was also found in participants with increased skeletal muscle mass in aHIIT group (r = 0.665, p = 0.002). Moreover, the change in VO2max was positively correlated with the change in FMD (r = 0.568, p < 0.001). In conclusion, both aHIIT and aMICT can raise aerobic capacity among OOYA. Importantly, aHIIT offers a time-efficient option to improve vascular function in OOYA, whereas aMICT may be preferable when the primary goal is to lower resting heart rate.