Figure captions

Fig. 1 Location of sampling sites along the Danube (29 sites, red circles) and tributaries (18 sites, black triangles) near their confluence with the Danube.
Fig. 2 Longitudinal change in species richness along the Danube (blue line) and tributaries (red dots). Occurrences of food/aquarium fish at sites along the Danube (blue bars) and tributaries (red bars).
Fig. 3 Boxplot comparison of the taxa richness obtained from eDNA (red) and (TEF) samples at the 18 common sites. For TEF, richness is expressed at the specific-species level (dark blue) and following the taxonomic assignment used for eDNA taxa (species or species group, light blue).
Fig. 4 Between-site variability of teleo-DNA concentrations in the Danube (blue line) and the tributaries (red dots) (Fig. 4a). Relationship between teleo-DNA concentrations and mean annual waterflow at the different sites from the Danube (blue dots) and tributaries (red dots) (Fig 4b).
Fig. 5 Comparison between eDNA and traditional electrofishing methods (TEF) at the 18 common sites sampled by both methods. Regressions (type II) of teleo-eDNA concentration (mitochondrial DNA copies/L) on fish biomass (Fig. 5a) and fish density (Fig 5b) estimated by TEF. Regressions (type II) of species-specific eDNA concentration on species-specific biomass (Fig 5 c) and species-specific density (Fig 5d).
Fig. 6 Number of eDNA copies per litre of taxa detected from the source to the mouth of the Danube River (in km). Only species with a relative abundance greater than one per thousand are represented. The size of the square is a function of the concentration of the corresponding taxa-specific eDNA per litre at a given site (see Supplementary Tab 1 for taxa abbreviation list). The separation of the Upper-, Middle- and Lower-Danube sections (vertical red lines) are based on the locations of the Gabcikovo dam (KM 1029) and the Iron Gate dams I and II (KM 1908 and KM1987 respectively)47.
Fig. 7 Plot of the number of taxa detected by eDNA against the number of teleo-DNA copies per sample for the 47 sites. Fitted curves from parameters estimated from a non-linear mixed model at the population level (black line) and individual level (red lines: tributaries, blue lines: Danube River). Longitudinal distribution of species.