Upland rivers across Europe still exhibit undisturbed conditions and represent a treasure that we cannot afford to lose. We hypothesize that the combination of pristine and modified conditions could demonstrate biological responses along the stressor gradients. Thus, the response of aquatic macrophyte communities to anthropogenic stressors along upland rivers in Bulgaria was studied. Six stressors were selected out of 36 parameters grouped into hydromorphological, chemical variables and combined drivers (catchment land use). The stressors strongly affected species richness on the basis of biological type (bryophytes vs. vascular plants) and ecomorphological type (hydrophytes vs. helophytes). Hydrological alteration expressed by the change of the river’s base flow and altered riparian habitats has led to a suppression of bryophytes and a dominance of riverbank plant communities. Seventy-five percent of mountain sites were lacking bryophytes, and the vegetation at semi-mountainous sites was dominated by vascular plants. It can be concluded that hydropeaking, organic and inorganic pollution, and discontinuous urban structures caused important modifications in the aquatic macrophyte assemblages. Macrophyte abundance and the biological and ecomorphological type of aquatic macrophytes reflect multi-stressor effects in upland rivers.