In Portugal, more than 150,000ha of eucalypt plantations are managed under best management practices (BMP), in compliance with international certification systems. Some of these forestry areas extend to streams, and the riparian areas are thus protected from productive land uses. However, many other eucalypt plantations present riparian zones that are not managed under BMP and are often occupied by agricultural uses. To test the effects of forest management on physical habitats and fish assemblages in Iberian eucalypt streams, we selected three different stream reach types: (1) reaches in catchments dominated by native vegetation associations, and presenting semi-natural riparian zones (reference-REF); (2) reaches surrounded by certified eucalypt plantations (i.e., managed under BMP), and consequently, presenting protected riparian buffer zones (PRZ); and (3) reaches surrounded by eucalypt plantations (dominant) and some oak forests, and presenting disturbed riparian zones with agricultural land use (DRZ). All sites represented small, low-gradient, warmwater streams in Central Portugal (Tagus basin), and their upstream land cover was dominated by natural/semi-natural uses. PRZ sites were abiotically similar to REF sites, although PRZ sites generally presented lower potential cover for fish and tended to support a riparian vegetation that was a little more fragmented. PRZ sites supported fish assemblages that were similar to those in reference reaches, although at the functional level we found a higher abundance of native invertivores in REF sites. DRZ reaches, on the other hand, differed substantially from the other two groups. DRZ sites presented disturbed riparian vegetation (removal or substitution of native trees by exotic and/or non-woody species), eroded and modified channels, and a degradation of stream habitats (lack of riffle–poll complexes, higher silt contents, and lower potential cover for fish). The fish assemblages were also quite different, with a higher abundance of alien specimens (mainly Gobio lozanoi) and generalist spawners, and a lower proportion of native invertivores and lithophils. Riffles and morphological alteration explained the greatest proportion of variance in species composition. Our study showed that protecting stream riparian zones by implementing BMP may mitigate the effects of eucalypt forestry on Iberian fish assemblages. However, given that there are a few differences in physical condition and biological integrity between streams associated with certified plantations and reference streams we suggest additional riparian management measures in the certified areas, such as restoration of the native vegetation, removal of alien plants, and improvement of the stream habitat.