The aquatic environment represents an adequate and safe alternative for children with overweight to exercise. However, the magnitude of the vertical ground reaction force (Fz) during these exercises is unknown in this population. Therefore, our study aimed to compare the Fz during the stationary running exercise between the aquatic and land environments in children with overweight or obesity. The study is characterized as a cross-over study. Seven children, two with overweight and five with obesity (4 boys and 3 girls; 9.7 ± 0.8 years), performed two experimental sessions, one on land and another in the aquatic environment. In both conditions, each participant performed 15 repetitions of the stationary running exercise at three different cadences (60, 80, and 100 b min−1) in a randomized order. Their apparent weight was reduced by 72.1 ± 10.4% on average at the xiphoid process depth. The peak Fz, impulse, and loading rate were lower in the aquatic environment than on land (p < 0.001). Peak Fz was also lower at 80 b min−1 compared to 100 b min−1 (p = 0.005) and loading rate was higher at 100 b min−1 compared to 80 b min−1 (p = 0.003) and 60 b min−1 (p < 0.001) in the aquatic environment, whereas impulse was significantly reduced (p < 0.001) with the increasing cadence in both environments. It can be concluded that the aquatic environment reduces all the Fz outcomes investigated during stationary running and that exercise intensity seems to influence all these outcomes in the aquatic environment.