Freshwaters are under accelerated human pressure, and mollusk communities are among its most sensitive, threatened, and valuable components. To the best of our knowledge, the overall effects of damming, environment, space, time, and invasive alien mollusk species, on structural and functional responses of native mollusk communities were not yet compared. Using historical information and recent data from a river, we aimed to investigate and disentangle these effects and evaluate the differences in structural and functional responses of natives and alien invasives to the same predictors. Variation partitioning showed that alien species were as important predictors as were environmental factors and time in explaining species composition of native freshwater mollusk communities. Aliens were more independent of environmental conditions than natives and responded to different drivers, partially explaining their invasion success. The increased abundance of some alien gastropods was positively related to taxonomic diversity, while certain alien bivalves were negatively associated with the functional diversity of native communities. We introduce a cumulative variation partitioning with multiple response (native and alien) and predictor matrices, along with a diagram to show their relations, advocating for a conceptual shift in future community ecology, from “variables to matrices” and from “multivariate analyses to multi-matrix statistical modeling”.