In a greenhouse, seven identical small-scale ecosystems, simulating hydrologically isolated lentic soft waters, were exposed to different artificial rain solutions during a 2-year period. Two major types of rain were used, one being sulphuric acid rain (pH 5.6–3.5) containing nitrate, the other being rain (pH 5.6) containing ammonium sulphate. The treatments with ammonium sulphate, particularly, caused remarkable changes in water quality and flora. pH decreased down to 3.5, whereas both ammonium and sulphate accumulated. Nitrification of ammonium appeared to be the dominant acidifying process. Concentrations of Ca, Mg, Fe, Mn, Al, Cd and Zn increased as a result of acidification. In the acidified systems exposed to a high deposition of ammonium sulphate, typical soft water plants, such as Littorella uniflora (L.) Aschers., disappeared and a luxuriant growth of both Sphagnum cuspidatum Ehrh. ex Hoffm. and Juncus bulbosus L. occurred. The microflora community also altered remarkablym with the filamentous green algae, Oedogonium spp. and Mougeotia spp., becoming dominant. Implications for the quantitative importance of airborne ammonium-induced acidification and eutrophication of surface waters in The Netherlands are given. It is suggested that for the survival of the biocoenoses of oligotrophic soft waters, total inputs of acid and ammonium-nitrogen should not exceed 250 and 1380 mol ha −1 year −1, respectively. It is emphasized that internationally, more attention should be focused on the role of atmospheric ammonium deposition in the acidification problem.