The relative role of environmental and regional processes in determining patterns of biodiversity may vary across spatial scales. In inland aquatic communities, macrophytes and zooplankton have the potential to disperse over large spatial scales (hundreds of kilometres), but the role of environmental and regional processes in determining species richness (SR) at different spatial scales is poorly understood. To assess the relative importance of environmental and regional processes acting on both regional (within-region) and continental (among-region) scales, we surveyed 139 waterbodies in five geographic regions (Spain, Italy, the Netherlands, Scotland and Norway) and in each region measured environmental variables, descriptors of connectivity and SR of two aquatic taxa, namely aquatic plants and cladocerans. Analyses using boosted regression trees and generalised linear models, integrated with multiple imputation of missing data, indicated that both environmental and regional processes were related to local SR. Total phosphorus was the main environmental correlate of SR, showing a unimodal relationship with both taxonomic groups. Conductivity and lake depth were also related to cladoceran SR, and Secchi depth was related to aquatic plant richness. The SR of aquatic plants and cladocerans were significantly correlated, but this relationship was mainly indirect (i.e. determined by the effect of common environmental variables). The limited role of connectivity and space (lack of spatial autocorrelation in model residuals) relative to environment suggests that dispersal limitation is not as important as the environment in explaining richness patterns for both groups within regions. However, region identity strongly influenced SR, which suggests an important effect of biogeographic factors (e.g. the level of endemicity; the number of unique species in each region) and/or dispersal limitation at the continental scale. We conclude that environmental factors and biogeographic processes largely determine the patterns of local and regional SR in aquatic plants and zooplankton.