After centuries of extinction due to human persecution, Eurasian beavers Castor fiber L. have been released to Southern Europe in the last decades. Being ecosystem engineers, beavers have attracted great attention regarding restoration of aquatic and terrestrial ecosystems. Nonetheless, the effects of the species on aquatic invertebrates known to date are not univocal and mostly refer to central European riverine systems. Here, we evaluated the effects of beaver presence on aquatic macroinvertebrates for the first time in a Mediterranean riverine ecosystem, by applying a sound control‐impact sampling design and controlling for seasonal variation in macroinvertebrate assemblage composition. A significant variation in response to season was evident for macroinvertebrate communities, revealing distinct assemblages during spring and summer. Furthermore, the presence of beavers was also identified as a significant driver of species composition, as samples near the beaver dam showed significant variation from control sites. Macroinvertebrate community traits changed according to the relative position to the beaver dam, as control sites featured on average higher abundances of taxa with higher values of bioindication score, larger size, lower adaptation to drag, and were less frequently of introduced origins. Yet, these differences were strongly taxon‐ and season‐specific in their intensity and direction. Differences across sites were mainly driven by the relative abundances of few taxa—including both alien species and high environmental quality indicators—such as those from genera Potamopyrgus, Baetis, Habrophlebia, Ephemerella, Leuctra, and Radix, which explained about 70% of the observed divergence among conditions. Our results indicate that beavers and their engineering activity may induce highly variable species‐specific responses in macroinvertebrates, thus possibly representing a driver of environmental heterogeneity along Mediterranean rivers, and that both bioindicators and alien species may exploit such heterogeneity.