The purpose of this study was to analyze the acute effects of a standardized water training session on the shoulder rotators strength and balance in age group swimmers, in order to understand whether a muscle-strengthening workout immediately after the water training is appropriate. A repeated measures design was implemented with two measurements performed before and after a standardized swim session. 127 participants were assembled in male (n = 72; age: 16.28 ± 1.55 years, height: 174.15 ± 7.89 cm, weight: 63.97 ± 6.51 kg) and female (n = 55; age: 15.29 ± 1.28 years, height: 163.03 ± 7.19 cm, weight: 52.72 ± 5.48 kg) cohorts. The isometric torque of the shoulder internal (IR) and external (ER) rotators, as well as the ER/IR ratios, were assessed using a hand-held dynamometer. Paired sample t-tests and effect sizes (Cohen’s d) were used (p ≤ 0.05). No significant differences were found on the shoulder rotators strength or balance in males after training. Females exhibited unchanged strength values after practice, but there was a considerable decrease in the shoulder rotators balance of the non-dominant limb (p < 0.01 d = 0.366). This indicates that a single practice seems not to affect the shoulders strength and balance of adolescent swimmers, but this can be a gender specific phenomenon. While muscle-strengthening workout after the water session may be appropriate for males, it can be questionable regarding females. Swimming coaches should regularly assess shoulder strength levels in order to individually identify swimmers who may or may not be able to practice muscle strengthening after the water training.