Longitudinal-zonation hypotheses generally predict gradual changes in fish composition from upstream to downstream due to changes in habitat conditions, but largely disregard downstream effects on upstream segments. Floodplains of large rivers represent areas of high connectivity during flood periods and can act as stable refuges in dry seasons, which may attenuate deterministic constraints imposed by local conditions on fish assemblages in surrounding habitats. In this study, we investigated the effects of proximity to large rivers on taxonomic- and functional-diversity patterns of stream-fish assemblages in an extensive region of Central Amazonia. We sampled 31 headwater-stream reaches in nine catchments in the Purus and Madeira Rivers interfluve between December 2014 and March 2015. Ninety seven fish species from seven orders and 19 families were captured. The results indicate that distance to large rivers is more important than distance among sites and local conditions in explaining functional and taxonomic diversity of stream-fish assemblages at large spatial scales. We also found a decrease in taxonomic and functional richness towards headwaters, mainly related to the loss of benthic and sedentary species along the distance gradient. These species may be favored by the proximity to refuge areas and high resource availability near the floodplain. In contrast, upstream assemblages were mainly occupied by small-sized, nektonic species with higher dispersal capacity, highly dependent of allochthonous resources. Downstream effects could be detected for many kilometers upstream in hydrographic catchments and this reinforces the crucial role of connectivity between fluvial habitats in maintenance of stream-fish diversity patterns in the region.