In the initial stages of the long-term swimmers’ training, the age-related functional capability of athletes should be taken into account. The improvement of young swimmer’ skills should be done in terms of an integrated approach to the promotion of physical fitness. The article presents the results of the study of aerobic and anaerobic capacity of 11–12-year-old swimmers under the condition of maximum oxygen consumption (VO2max), the maximum amount of external mechanical work for 10s (VanT10), 30s (VanT30), 60s (MKMMD). For the scientific substantiation of the expediency of implementing the method of interval hypoxic training and elements of aquafitness in the training process of 11–12 year-old swimmers, it is necessary to investigate the indexes of functional preparedness of 11–12 year-old swimmers, depending on their gender. It has been found out that the level of aerobic productivity of the boys’ bodies equals “good”, and the girls’ – “excellent” according to Y.P. Pyarnat. Elements of aquafitness and interval hypoxic training are recommended to be applied to improving aerobic and anaerobic capacity of swimmers at the stage of initial basic training.