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This study aimed at unraveling the structure underlying the taxon‐richness matrix of shallow lakes. We assessed taxon richness of a large variety of food‐web components at different trophic levels (bacteria, ciliates, phytoplankton, zooplankton, fish, macro‐invertebrates, and water plants) in 98 shallow lakes from three European geographic regions: Denmark (DK), Belgium/The Netherlands (BNL), and southern Spain (SP). Lakes were selected along four mutually independent gradients of total phosphorus (TP), vegetation cover (SUBMCOV), lake area (AREA), and connectedness (CONN). Principal‐components analysis (PCA) indicated that taxon diversity at the ecosystem level is a multidimensional phenomenon. Different PCA axes showed associations with richness in different subsets of organism groups, and differences between eigenvalues were low. Redundancy analysis showed a unique significant …