Of all the environmental elements that influence the biological communities of rivers, water flow characteristics are undoubtedly the most important. Unfortunately, natural hydrological characteristics are increasingly threatened by human activities, especially in alpine or high mountain areas where there are numerous hydropower plants. In this study, we analysed the impact of hydrological alterations on the macroinvertebrate community of a lowland river in NW Italy. Specifically, we analysed the macroinvertebrate communities of an unaffected site by comparing them with those of a site subject to hydrological alteration. We adopted an approach that is not only taxonomic but also functional, allowing us to study a component of biodiversity that is generally less known. Our results show that the flow-altered site hosted a benthic community with lower species and functional diversity than the control site. Interestingly, we also detected a number of significant differences between the summer and autumn samples. In particular, examination of community-weighted mean (CWM) trait values reveals significant variation in body size, voltinism, substrate, locomotion, feeding habits and other traits between sites and seasons. The integration of taxonomic and functional approaches provides a comprehensive understanding of how human-induced hydrological variations can affect aquatic biodiversity and ecological functions.