The influence of the flood pulse on fish populations has been posited, but infrequently tested or quantified. Here, we tested the effect of habitat on population size, using Prochilodus nigricans as a case study species. Floodplain habitat was based on the littoral zone area occupied by P. nigricans to feed. The magnitude of this habitat in each hydrological year, the moving littoral (ML), was expressed as the sum of daily littoral areas during the advancing flood pulse, using satellite-based passive microwave data. Annual population size was estimated by age-class, using a dynamic age-structured model (MULTIFAN-CL) based on catches, effort, and fish length frequencies from the Manaus-based fishery over 12.75 years. The principal null hypothesis was that ML, using three lag times, had no effect on population size of a single age class of P. nigricans. The population size at 29 months of age was positively related (P=0.00030) to floodplain habitat (ML) earlier in the same year, when the fish were 21-27 months old. The result implies a density-dependent relationship for the population with respect to its feeding habitat. Potential mechanisms governed by flood pulse variation and habitat quality for this and other species utilizing floodplain habitats are discussed.