The negative impacts of big dams construction in the functioning of lotic ecosystems are relatively well known. However, it remains unclear the influence of small hydropower plants (SHP) in mountain aquatic ecosystems, namely in the Northeastern Portugal. The aim of this work was to evaluate the impacts of SHP, on the ecological quality of different watercourses. The ecological impact assessment was based on different methodologies that allowed to characterize the abiotic component, like physical and chemical water quality and the condition of aquatic and riparian habitats, and the biotic component, based on macroinvertebrate fish communities, according with the protocols of Water Framework Directive. During spring season of 2015 it was evaluated the ecological integrity of the upstream and downstream of each SHP, and several responsive metrics were found to detect changes in the overall biological quality of watercourses, particularly in locations located downstream of the SHP.