The data regarding somatic and physiological effects of sport-related physical activities in youth are limited. Moreover, whether exercise training is capable of increasing cardio-respiratory fitness remains a disputable issue. The study undertook to assess the effect of swimming training on cardio-respiratory fitness (CRF) and the development of physical traits in prepubertal boys, and to determine which of the traits is the best predictor of their CRF. Forty 10-year old prepubertal boys (10.5 ± 0.3 y) were divided into two groups (swimmers (SG), n = 20, and controls (CG), n = 20), which underwent anthropometric measurements and performed a 20 m shuttle run test (20 mSRT) semi-annually over a 3-year period. CRF indices (the number of 20 mSRT shuttles, maximal speed, and VO2max) were higher overall in the SG compared with the CG (p < 0.001). The values of the main physique variables increased faster in the CG, but the groups showed no differentiation of physical traits. In both groups, CRF indices were associated with the participants’ physical traits, the most strongly with the sum of four skinfold thicknesses in the SG and knee breadth in the CG. These results suggest that swimming training is a form of additional physical activity that improves prepubertal boys’ CRF but does not significantly affect their physical development. In using the 20 mSRT to assess the CRF of prepubertal boys, their physical activity level and age-related changes in body fatness need to be considered.