Flooding regulates the amount and quality of habitat available for fish populations in river-floodplains. Although previous studies assessed fish population responses to river hydrology, the processes by which flooding affects fish abundance and catch remain unclear. Here, we investigated whether degree of flooding affects abundance and catch of Colossoma macropomum, a long-lived, overexploited fish population of the central Amazon Basin. We computed the degree of flooding corresponding to the feeding area of young-of-the-year C. macropomum as the annual magnitude of the moving littoral zone (ML). We estimated abundance of age classes one, two, and three of C. macropomum using a modeling program based on catch, fishing effort, and fish length frequency data from the principal commercial fishery. We found that flooding positively and non-linearly affected abundance of the age-one cohort but not of older age classes. ML data corresponding to a late rising water phase in which zooplankton, seeds, and fruits dominated the diet provided the strongest effect on age-one abundance. However, flooding effects on total catch were not found, likely due to catches comprising several age classes. These results provide support to existing evidence that the magnitude of the moving littoral zone regulates abundance of juvenile fish. Because the ML quantifies food and habitat availability for various other fish species, it may constitute an important control of fish abundance in these systems. Management of these fisheries may be improved by adjusting fishing effort based on hydrology. More generally, the information also serves to assess the impacts of hydrological alterations (e.g., dams) on fish recruitment.