The main aim of this study was to compare the performance over different distances, the critical velocity (CV), and plasma acylcarnitines/amino acids of male and female adolescent swimmers. Moreover, we applied the complex network approach to identify which molecules are associated with athletes’ performances. On the first day under a controlled environment, blood samples were collected after 12 h of overnight fasting. Performance trials (100, 200, 400, and 800-m) were randomly performed in the subsequent four days in a swimming pool, and CV was determined by linear distance versus time mathematical function. Metabolomic analyses were carried out on a triple quadrupole mass spectrometer performing electrospray ionization in the positive ionization mode. No difference was observed between the performance of male and female swimmers. Except for 200-m distance (p = 0.08), plasma tyrosine was positively and significantly associated with the female times during the trials (100-m, p = 0.04; 400-m, p = 0.04; 800-m, p = 0.02), and inversely associated with the CV (p = 0.02). The complex network approach showed that glycine (0.406), glutamine (0.400), arginine (0.335), free carnitine (0.355), tryptophan (0.289), and histidine (0.271) were the most influential nodes to reach tyrosine. These results revealed a thread that must be explored in further randomized/controlled designs, improving the knowledge surrounding nutrition and the performance of adolescent swimmers.