Benthic algal flora of the River Danube is presented with implications for ecological status assessment. Structure of algal biofilms, species diversity, algal abundance, and biomass are described and discussed based on most recent algal investigations supplemented by methodological insight to community structure evaluation. Comparisons of literature data are provided. Seasonal and longitudinal changes of benthic algal assemblages are evaluated in terms of species abundance and biomass as well as community structure. In contrast to previous studies of Danubian periphyton that detected prevailing diatom abundance in the biofilms, recent research has found that cyanobacteria and green algae dominated almost along the whole Danube stretch. Ecological status of the entire Danube stretch is evaluated by means of the diatom-based “Indice de Polluosensibilite Specifique” (IPS), which showed distinct differences between the upper and middle section of the River Danube indicating longitudinal increase of general degradation of aquatic environment and increasing nutrient concentrations. The overall indication of ecological status varied between good and moderate.