To describe accurately the mineral changes (Ca and Mg) provoked by swimming, the aims of this study were to analyze those tissues that, with regard to their mineral content, can better classify individuals performing both swimming until exhaustion and swimming as training and to know the shifts of these minerals between different tissues after a single session of swimming until exhaustion and after training. Wistar rats were distributed into 12 groups, six male and six female (N = 10): 1) control rest group (CR); 2) trained rest group (TR); 3) control exercise group (CE); 4) trained exercise group (TE); 5) control recovery group (CER) and 6) trained recovery group (TER). The most informative tissues of Ca and Mg compartmental shifts during exercise have been determined. Discriminant analysis selected heart Ca, muscle Ca and bone Ca, bone Mg, erythrocyte Mg, and serum Mg as the most significant variables. The animals were classified by means of two canonical axes: the first one relates to training situation and sex, and the second one shows the special characteristics of trained male rats. Another independent discriminant analysis applied to male and female groups separately showed that the first canonical axis (control/trained) is basically defined by heart Ca, bone Ca, and erythrocyte Mg (male), and by heart Ca, bone Ca, and bone Mg (female), while the second axis, related to the exercise situations, is defined by the serum Mg levels in both sexes. We think that discriminant analysis is a statistical method capable of explaining physiological processes and classifying individuals performing exercises of different length. It suggests that the homeostasis of Ca and Mg is somewhat different for males and females. Serum magnesium must be considered to distinguish exercise situations. The analysis of these tissues could inform us about the mineral status of the rats and then we could correct possible deficiencies in our research. In this work we have only found different mineral redistributions among tissues. The trained animals have a better mineral recovery capacity than the untrained ones. Training has a different physiological repercussion in male and female rats on the basis of their respective maximal swimming times after training and their mineral behavior.