Abstract In the Netherlands, atmospheric deposition of ammonia compounds, particularly ammonium sulphate, is an important source for the acidification of oligotrophic soft waters. As a consequence, the acidified waters are generally nitrogen enriched, ammonium being the dominant N form. In this study, it is examined how this alteration in the nitrogen household affects the aquatic plant communities in acidifying waters. The uptake of ammonium and nitrate by leaves and roots of two groups of freshwater plants has been studied using glass incubation chambers. The forst group ( Littorella uniflora (L.) Aschers.; Lobelia dortmanna L.; Luronium natans (L.) Raf.; Echinodorus ranunculoides (L.) Engelm.) is characteristic of nitrogen-poor soft waters, whereas the second group ( Juncus bulbosus L.; Sphagnum flexuosum Dozy & Molk.; Agrostis canina L.; Drepanocladus fluitans (Hedw.) Warnst.) often occurs in dense stands in nitrogen-enriched, acid waters. Both groups have typical adaptations to the nitrogen condition of their aquatic environment. The soft-water species show a nitrate-dominated (63–73%) nitrogen utilization, with the roots as the major (83%) uptake site. Moreover, they are able to survive at very low nitrogen concentrations. The acid-tolerant species have an ammonium-dominated (85–90%) nitrogen utilization, with the leaves as the major (71–82%) uptake site. This group profits from the increased ammonium levels in acid waters. It is concluded that in the case of acidification increased ammonium concentrations additionally account for the suppression of typical soft-water communities by communities dominated by Juncus bulbosus and Sphagnum spp.