Abstract Peacock basses (Cichla spp.) have been introduced in impoundments for decades, and their negative impacts on the native fish fauna have been documented. However, previous studies largely focused on the overall responses of fish assemblages, often neglecting specific predator–prey interactions and the underlying effects of environmental characteristics. Here, the effects of peacock bass introduction on the size structure (<120, 120–180 and >180 mm in total length) of fish assemblages in reservoirs of the Paraíba do Sul river basin were assessed. The abundance and time since the introduction of peacock basses were used as predictors, together with reservoir features, limnological variables and habitat composition as potential influencing factors. Descriptors of the overall community (richness, abundance and species composition) were only marginally associated with the occurrence of peacock basses. However, small and (to a lesser extent) medium‐sized fish were adversely affected by the abundance and introduction time of peacock basses. Two pelagic native characids – namely Astyanax cf. bimaculatus and Oligosarcus hepsetus – were the most affected. Redundancy analysis showed that reservoir age and macrophyte cover were the best predictors of fish assemblage composition. Older reservoirs and reservoirs with a higher cover of macrophytes showed a greater abundance of catfish and characids, respectively. Peacock basses appear to affect fish assemblages through predation on small fish. Therefore, analyses of assemblages by size are recommended, as the use of overall assemblage descriptors may not be sufficient to capture the adverse effects of peacock basses. Moreover, these findings underscore the importance of conserving and restoring habitats in littoral zones, which function as refuges for native fish species in reservoirs. Further educational and management measures are warranted to prevent the spread of peacock basses to other reservoirs in Brazil.