Recording and assessment of aquatic macrophytes was a request for the Joint Danube Survey 2 (JDS2). New insight regarding occurrence, abundance and specific distribution of macrophytes was based on methodological adaptations better adjusted to the size of this large European river and permitted more appropriate statistical interpretation. Regarding the ecological status of sampling stretches, an intentional, preliminary way of interpretation is provided, respecting trendsetting new international literature. Due to longer river stretches recorded, a higher number of species was detected in JDS2. Each of the ten official river sections showed an individual character of the macrophyte vegetation. Results of JDS2 macrophyte survey are put in relation with international literature and side effects are discussed, which are of relevance when assessing macrophytes in large rivers for purposes of science, European Water Framework Directive or regarding conservation issues.