Many studies have assessed the effects of large dams on fishes but few have examined the effects of small obstacles. Fishes were sampled and environmental variables were characterized at 28 sites in two Iberian streams, 14 located immediately downstream, upstream and between five small obstacles at river Muge and 14 at river Erra, considered as the reference stream. Multivariate analysis indicated that habitat variables like current velocity and depth, but not physicochemistry, were mainly responsible for site groups' discrimination in both streams. The reference stream exhibited a longitudinal gradient of current velocity that, however, was not strong enough to cause significant changes in the fish assemblage's composition and structure. By successive and drastically repeating this gradient near each structure, the obstacles stream presented differences in fish fauna between the three site types. Lentic upstream sites presented higher density of limnophilic, omnivorous and exotic species, like gudgeon Gobio lozanoi, which are well adapted to this type of habitat. Downstream and between obstacles sites were characterized by the dominance of rheophilic and invertivorous taxa, especially barbel Luciobarbus bocagei. Richness metrics did not differ among site types, but diversity was higher in sites located between the obstacles away from its direct influence, where the habitat diversity was higher. Contrarily to upstream sites, downstream and between obstacles sites were similar in many of the studied features to the reference stream, implying that this type of structures cause a higher modification in the upstream fish community. This study suggests that the effects of small obstacles on habitat and fishes are similar, in some extent, to those reported for larger dams, providing important considerations for riverine ecosystem conservation efforts.