The expansion of agriculture in the southeast Amazon-Savanah transitional area has greatly decreased forest cover and influenced stream structure and functioning. We assessed the effects of forest cover loss on the integrity of streams by assessing stream physical conditions and the taxonomic and functional diversity of fish assemblages in this transitional area. We hypothesize that low forest cover, especially adjacent to streams, results in poor physical conditions (e.g., warmer temperatures, less physical structure, etc.), which in turn will decrease the taxonomic and functional diversity of fish assemblages. We detected that loss of forest cover negatively affects natural stream conditions and reduces the functional diversity of fish assemblages, but we did not find a strong effect on taxonomic diversity. Ambush and stalking predators, diurnal surface pickers (groups that exhibit opportunistic life history strategies), grazers, pickers, and browsers (groups that exhibit equilibrium life history strategies) were the functional groups with the strongest relation to altered environments. These groups can explore different niches, both with natural characteristics or altered by human activities. Our results suggest that the preservation of riparian zones can minimize the loss of specialized fish species in assemblages of Amazon-Savannah stream systems.(AU)