Land-cover change often shifts the distribution of biomass in animal communities. However, the effects of land-cover changes on functional diversity remain poorly understood for many organisms and ecosystems, particularly, for floodplains. We hypothesize that the biomass distribution of fish functional diversity in floodplains is associated with land cover, which would imply that fish traits affect behavioral and/or demographic responses to gradients of land cover. Using data from surveys of 462 habitats covering a range of land-cover conditions in the Amazon River floodplain, we fitted statistical models to explain landscape-scale variation in functional diversity and biomass of all fish species as well as subsets of species possessing different functional traits. Forest cover was positively associated with fish biomass and the strength of this relationship varied according to functional groups defined by life history, trophic, migration, and swimming-performance/microhabitat-use traits. Forty-two percent of the functional groups, including those inferred to have enhanced feeding opportunities, growth, and/or reproductive success within forested habitats, had greater biomass where forest cover was greater. Conversely, the biomass of other functional groups, including habitat generalists and those that directly exploit autochthonous food resources, did not vary significantly in relation to forest cover. The niche space occupied by local assemblages (functional richness) and dispersion in trait abundances (functional dispersion) tended to increase with forest cover. Our study supports the expectation that deforestation in the Amazon River floodplain affects not only fish biomass but also functional diversity, with some functional groups being particularly vulnerable.