An intensively debated issue in ecology is whether variability in the patterns of diversity of different groups of organisms is congruent in space, a phenomenon referred to as cross-taxon congruence. Whereas this has been previously mainly tested in terms of taxonomic dissimilarity, the role of ecological processes in determining the congruence of multiple diversity facets (i.e. alpha- and beta-diversity, taxonomic, and functional) remains poorly understood. We used a data set of observation records for 469 macrophyte and 543 fish taxa at the catchment-scale from the existing literature and data bases to test the existence of multi-faceted congruence patterns and investigate the variables driving them across 214 catchments covering the whole Chinese mainland. We found cross-taxon congruence of multiple diversity aspects between fish and macrophyte communities. The energy (i.e. diversity is limited by energy availability), area/environmental heterogeneity (i.e. diversity is higher in larger and more heterogeneous areas), and dispersal (i.e. diversity is driven by dispersal) hypotheses were all significantly attributed to the cross-taxon congruence, suggesting the existence of key repeated mechanisms underlying assemblage organisation. Our study provides new evidence that can further our understanding of the factors and underlying processes explaining cross-taxon congruence patterns at broad spatial scales in the freshwater realm, the studies of which significantly lag those in the marine and terrestrial realms. The present findings also provide important baseline information for freshwater conservation initiatives.