This study aimed to determine the injury patterns associated with training activities in elite South Korean aquatic sports athletes training for the Olympic Games. From 2012 to 2019, we prospectively collected data on elite aquatic sports athletes at the Korea National Training Center. The athletes were assessed by four sports medicine doctors, and data were stratified according to sex, aquatic style, injury body location, and injury severity. Chi-square tests were used to compare groups. Injury rates was expressed as rate ratios with 95% confidence intervals. Annually, the center hosts an average of 42 elite aquatic athletes spread over four aquatic styles. We recorded 797 injuries in total (annual average: 2.37 injuries/athlete), during training sessions, 57.1% of which were mild injuries. For all athletes, most injuries occurred in the upper limb (35.9%), followed by the lower limb (31.0%), the trunk (24.5%), and the head and neck (8.7%). Aquatic style significantly influenced injury body location and severity for both male and female athletes (injury body location: p < 0.001 and p < 0.010, respectively; injury severity: p = 0.027 and p < 0.001, respectively). In general, male and female athletes experienced a comparable risk of injury (rate ratio: 1.15; 95% confidence intervals: 0.53-2.46). Among the male and female South Korean elite aquatic athletes training for the Olympic Games, most injuries were mild and occurred in the upper limb, and aquatic style influenced injury body location and severity.