Niche and neutral processes drive community assembly and metacommunity dynamics, but their relative importance might vary with the spatial scale. The contribution of niche processes is generally expected to increase with increasing spatial extent at a higher rate than that of neutral processes. However, the extent to what community composition is limited by dispersal (usually considered a neutral process) over increasing spatial scales might depend on the dispersal capacity of composing species. To investigate the mechanisms underlying the distribution and diversity of species known to have great powers of dispersal (hundreds of kilometres), we analysed the relative importance of niche processes and dispersal limitation in determining beta-diversity patterns of aquatic plants and cladocerans over regional (up to 300 km) and continental (up to 3300 km) scales. Both taxonomic groups were surveyed in five different European regions and presented extremely high levels of beta-diversity, both within and among regions. High beta-diversity was primarily explained by species replacement (turnover) rather than differences in species richness (i.e. nestedness). Abiotic and biotic variables were the main drivers of community composition. Within some regions, small-scale connectivity and the spatial configuration of sampled communities explained a significant, though smaller, fraction of compositional variation, particularly for aquatic plants. At continental scale (among regions), a significant fraction of compositional variation was explained by a combination of spatial effects (exclusive contribution of regions) and regionally-structured environmental variables. Our results suggest that, although dispersal limitation might affect species composition in some regions, aquatic plant and cladoceran communities are not generally limited by dispersal at the regional scale (up to 300 km). Species sorting mediated by environmental variation might explain the high species turnover of aquatic plants and cladocerans at regional scale, while biogeographic processes enhanced by dispersal limitation among regions might determine the composition of regional biotas.