Anthropogenic transformations of the catchment area and river bed are responsible for the changes in the geomorphology of the river valleys, the hydrological regime of rivers, the river continuum, as well as the river ecosystems. Transformed valleys offer ecological niches that are different from the natural ones, which are inhabited by organisms that should not be present in a high density in rivers or streams. We aimed to answer the question of whether the communities of microinvertebrates are indicative of anthropogenic transformations taking place in the river bed and in the catchment area. For this purpose, the study was conducted on the six upland rivers in the drainage of the Douro River, Northern Portugal. According to our results, for the diversity and abundance of microinvertebrate communities (Rotifera, Cladocera, and Copepoda), the characteristics of the catchment area are not as important as the transformation of the riverbed. The abundance of microinvertebrates is related to natural processes that are described in the river continuum concept; however, dams higher than 10 m drastically reorganized communities from benthic to typically pelagic. Large dams (>10 m) built on small rivers caused an apparent increase in species richness, as these species are the same as those found in large rivers. Therefore, the river networks were homogenized both in relation to microinvertebrate abundance and taxa. Less transformation of the riverbed (lack of impoundments) favors the greater Simpson diversity of microinvertebrates, but the density is then very low. Our results show that dams have a large influence on the communities of microinvertebrates in the river, which in turn can cause cascading spatial changes to the river ecosystem.