Abstract In order to monitor recovery from acidification caused by acid atmospheric deposition, desmids and water chemistry were sampled in three Dutch moorland pools regularly from 1978 to 2014. Reference desmid samples from the early twentieth century were retrieved from old collections. Changes of the desmid assemblages were assessed by analyses of traits, including indicator values for pH and total phosphate, conservation value, cell volume and surface/volume (s/v) ratio. Direct correspondence analysis (DCA) traced relations between desmids and environmental variables. Between 1916 and 2014, species composition altered due to changes in acidifying atmospheric deposition: The change was most pronounced in pools with relatively flat shores exposed to the atmosphere in extremely dry summers. After the dry summer of 1921, changes were slight, but after the dry summer of 1976, changes were dramatic, when the sulphur and nitrogen compounds stored in the water bottom oxidized and acidified the water. The conservation value declined sharply but increased again until the 1990s, partly due to the decrease in acidifying deposition. Although the acid atmospheric deposition continued to decline until the early 21th century, the conservation value declined again, as did the stability of the desmid assemblages. It is likely that internal eutrophication (nutrients), presence of toxic substances (such as hydrogen sulphide), the decline of aquatic macrophytes (substrate), shading by afforestation (light) and/or reduced supply of carbon dioxide (due to decreased local seepage) play a role. The chemical dynamics due to the large stock of sulphur and nitrogen compounds will hamper the development of rare desmids, bound to stable environmental conditions.