In order to evaluate latitudinal differences in the relationship of phytoplankton biomass and diversity with environmental conditions in shallow lakes, we sampled 98 shallow lakes from three European regions: Denmark (DK), Belgium/The Netherlands (BNL) and southern Spain (SP). Phytoplankton biomass increased with total phosphorus (TP) concentrations and decreased with submerged macrophyte cover across the three regions. Generic richness was significantly negatively related to submerged macrophyte cover and related environmental variables. Zooplankton:phytoplankton biomass ratios were positively related to submerged macrophyte cover and negatively to phytoplankton generic richness in DK and BNL, suggesting that the low generic richness in lakes with submerged macrophytes was due to a higher zooplankton grazing pressure in these regions. In SP, phytoplankton generic richness was not influenced by zooplankton grazing pressure but related to conductivity. We observed no relationship between phytoplankton generic richness and TP concentration in any of the three regions. The three regions differed significantly with respect to mean local and regional generic richness, with BNL being more diverse than the other two regions. Our observations suggest that phytoplankton diversity in European shallow lakes is influenced by submerged macrophyte cover indirectly by modulating zooplankton grazing. This influence of submerged macrophytes and zooplankton grazing on phytoplankton diversity decreases from north to south.