Life‐history traits of Pygocentrus nattereri were compared in two populations inhabiting connected tributaries of the upper Madera River: the white water Mamoré River and the clear water Iténez River. As white waters provide better trophic conditions than clear waters, the size at maturity, fecundity, reproductive effort, condition and growth of P. nattereri should be greater in the more productive white water river (Mamoré) than in the less‐productive clear water river (Iténez). Breeding periods were highly seasonal and similar in both rivers and under strong influence of photoperiod. Oocyte size‐frequency distributions, together with the frequent occurrence of recovering females indicated that an individual female spawns at least twice during the breeding season. As predicted, fish of the Mamoré were significantly larger at maturity and had higher fecundity and condition factor values than those of the Iténez. Fish from both rivers matured as yearlings. The higher growth potential of females was better expressed in the Mamoré than in the Iténez, where growth differences between sexes were weak. Females had a significantly better growth in the Mamoré than in the Iténez. The observed life‐history traits associations were consistent with the hypothesis of better trophic conditions in the Mamoré. In addition, previous genetic analyses evidenced that the colonization of the two basins is recent and that extant populations have very similar genetic backgrounds. This suggests that the observed variations in life‐history traits of P. nattereri are not related to historical factors (genetic drift) between two phylogeographically distinct lineages, but rather due to the contrasting environmental conditions in the white and clear waters.