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In recent years, species richness and diversity in aquatic ecosystems has declined as environments are increasingly impacted by anthropic actions. Freshwater prawns are well adapted to survive in a disturbed and heterogeneous environment. For instance, Amazon river prawn (Macrobrachium amazonicum) populations vary in migratory behavior between rivers and estuaries, depending on factors such as dams. However, there is limited information on the influence of environmental conditions on life‐history traits of this species, which we investigate here using two distinct and unconnected aquatic systems, a dammed river and an estuary, in the eastern Brazilian Amazon. The biological characteristics of M. amazonicum populations in the two environments were compared and related to environmental parameters, which differed significant differences between the two environments and between seasons. Dissolved oxygen, precipitation, and temperature varied most significantly with the seasons in both the estuary and river. M. amazonicum prawns in the estuary were larger and heavier than those in the river during rainy periods. The mass–length ratios and condition factor varied significantly between the M. amazonicum populations in the estuary and river, with negative allometric growth (grows faster in length than in weight) predominating in both populations, and condition factor was better in the estuary for males and in the river for females. The relative frequencies of occurrence of the different female maturation stages and the male morphotypes were related to precipitation and turbidity in both environments and also to salinity in the estuary. In these two distinct aquatic systems, the abiotic parameters determined by the seasonal precipitation cycle profoundly influenced the development of this crustacean, despite its ecological plasticity. Overall, the study showed that river damming triggered environmental changes in the freshwater river ecosystem and played a key role in determining the life‐history characteristics of M. amazonicum in these contrasting aquatic systems. [ABSTRACT FROM AUTHOR]