Riparian deforestation degrades stream habitats, altering fish assemblages’ structure, and composition. In contrast, secondary riparian forests can recover stream habitats and fish assemblages as they recover structural attributes and ecological processes. We evaluated whether the amount and condition of secondary riparian forests were important to conserve fish assemblages in 49 streams sites in eastern Amazonia. We related fish assemblage taxonomic and functional measures to riparian forest amount plus different habitat metrics using regression analysis. We compared assemblage measures among reference forests, abandoned pastures (open canopy), and secondary forests (closed canopy) using ANOVA tests. The amount of secondary forests had little influence on fish assemblages. Species richness, diversity, and functional richness were higher in pasture than in reference sites but returned to pre-disturbance conditions in secondary sites. However, functional evenness was lower in pasture streams and did not recover after secondary forest regrowth. Our results show that secondary riparian forest condition is important to recover some aspects of fish assemblages. However, streams bordered by these forests may have impoverished fish assemblages because some lost sensitive species may take longer to return. Avoiding riparian deforestation is the best strategy to reduce losses in aquatic biodiversity and ecosystem functions in tropical agricultural landscapes.