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Water currents are among the strongest environmental variables determining the occurrence and/or abundance of aquatic plants and the European Water Framework Directive (WFD) considers river morphology and current conditions important aspects of reference conditions. We used the database of the Joint Danube Survey JDS-2, organised by the International Commission for the Protection of the Danube River (ICPDR, Vienna), to assess the relationship between water flow velocity and the occurrence and abundance of aquatic macrophyte to be species along the navigable reach of the Danube River. Species abundance was assessed in accordance with European Standard EN 14184-2003. Flow velocities were assessed close to the plant stands and estimated in 4 classes, worked out in earlier studies in combination with flow meter measurements, which is appropriate for the conditions in this large river. Statistical analysis revealed that only survey units with either no visible flow or those with fast flow were characterised by indicator species with high significance. Still water conditions or barely visible flow (flow class 1) were indicated by Potamogeton friesii , Nitellopsis obtusa and Trapa natans , and by Potamogeton perfoliatus , Potamogeton nodosus and Stuckenia pectinata . Lemna minor , indicative for flow class 1 as well, was detected in all the other flow classes, too: in all these cases it established its stands closely intermingled with other aquatic species. For survey units with slow (flow class 2) or intermediate flow (flow class 3). No statistically significant indicator species could be determined. The highest flow velocities (flow class 4) were significantly indicated by Fissidens rufulus , Cinclidotus fontinaloides and Cinclidotus riparius . Occurrence of aquatic mosses was also highly related to the Berger–Parker dominance index in NMDS analysis. In the same analysis, but towards the smallest flow velocities, the majority of vascular species and the Simpson diversity index were closely related. The spectrum of life forms was considerably reduced under medium and high flow velocity conditions. With regard to Simpson species diversity, our analysis indicates an agglomeration of diversity in the Middle Danube reach that includes the Iron Gates impoundment. Our results offer a first look at the macrophyte/water flow relationship of a very large river in Europe, the Danube.