In times of rapid environmental changes, baseline biodiversity data are crucial for management. In freshwaters, fish inventories are commonly based on the capture and morphological identification of specimens. The sampling of environmental DNA (eDNA) provides an alternative to assess diversity across large catchments. Here, we used extensive historic data of fish communities collected across 89 river sites in all major catchments of Switzerland and compared their diversity and community composition to a single campaign of eDNA and electrofishing, respectively. Locally, we found that eDNA provided diversity estimates similar to the integrated historic richness, while the electrofishing campaign captured a significantly lower local richness. Fish species locally recorded by electrofishing were nested (Jaccard's dissimilarity index) within the respective eDNA community for most sites. Finally, eDNA sequence reads positively correlated with the overall electrofishing biomass. Despite the congruences, the eDNA data did not correlate well with the electrofishing water quality index. Overall, eDNA was more accurately assessing overall diversity than a simultaneous electrofishing campaign, but yet cannot be directly used to calculate fish-based water quality indices.