In recent decades, many aquatic ecosystems in Europe and North America have experienced reduced inputs of nutrients and acidifying substances because of improved sewage treatment and reduced emission of sulphur oxides. We evaluated the consequences of these efforts to changes in water chemistry, species richness and community composition of aquatic macrophytes in 56 lakes in Denmark around 1990 and again around 2010. Reductions in lake water concentrations of phosphorus and nitrogen were strongest in eutrophic and hypertrophic lakes, for example, lakes which had been heavily affected by domestic sewage. These changes translated into decreased algal biomass in the most eutrophied lakes. Oligo‐ and mesotrophic lakes did not change significantly in terms of nutrients or algal biomass. Water clarity increased across all lakes but not significantly in specific trophic lake groups. Alkalinity and pH increased significantly (up to 2 pH‐units) in low‐alkaline lakes, while well‐buffered high‐alkaline lakes (>0.5 meq/L) did not show any change. Macrophyte species richness per lake increased, on average, by 13% during the 20‐year study period. The increase was strongest in species preferring nutrient‐rich conditions and could be directly attributed to reductions in phytoplankton biomass in lakes of medium water clarity. The similarity among all lakes in terms of species composition increased over the study period. This development was closely related to higher average species richness and was mainly caused by recolonisation of lakes, recovering from past eutrophication, by relatively common species (e.g., Lemna trisulca, Sparganium emersum and Potamogeton berchtoldii). Higher pH in low‐alkaline lakes was accompanied by a shift from acid‐tolerant to more acid‐sensitive species. Our results demonstrate that investment in pollution control has been successful in terms of markedly improving water quality of lakes and, with a time lag, macrophyte species richness. Although relatively common species have spread across lakes and resulted in homogenised macrophyte communities, continued efforts to reduce pollution could ensure the survival of rare specialist species and perhaps even increase their abundance in the future.