The competitive ability of hybrids, compared with their parental taxa, can cover a wide fitness range from poor to superior. For example communities of the Daphnia galeata-hyalina-cucullata species complex often show hybrid dominance. We tested whether taxa composition of 43 European lakes inhabited by this species complex can be explained by habitat characteristics (e.g. size descriptors, trophy level) or geography. We found that D. galeata occurs more frequently south of the Alps, whereas D. hyalina and D. cucullata are found more in the north. Lakes with D. galeata dominance had higher temperatures whereas D. hyalina dominance could be attributed to low phosphorus loads. The dominance of F1-hybrids, however, was not explainable with current environmental variables. In a subset of 28 lakes, we studied the impact of eutrophication history on F-hybrid success. Lakes with the highest trophic state in the past tended to be dominated by F1-hybrids. Our data demonstrate that human-mediated habitat disturbance (eutrophication) has facilitated hybrid success and altered the Daphnia taxon composition across lakes. At the same time, specific habitat conditions might provide a refuge from hybridization for native genotypes.