Western European coastal dune landscapes are naturally dynamic and ever changing. However, in the past 100 years coastal dunes have become more stable and encroached by sand-fixating grasses and shrubby vegetation. The drivers of these changes are primarily due to human exploitation with deliberate planting for coastal protection and nitrogen deposition, mainly from agricultural sources. The effects of these changes on terrestrial plant communities in dune landscapes are well documented; they are becoming more homogenous and species poor especially due to the loss of specialized pioneer species. However, much less is known about the effects on the aquatic plant communities in the dune landscape. Here we studied the composition of plant communities in 38 shallow dune lakes in Northwest Denmark, with the aim to identify the effect of stabilization and vegetation encroachment on the aquatic plant communities. Fine benthic and dissolved organic matter (FBOM and DOC) along with lake type (permanent/temporary) was among the main explanatory factors for specialized dune lake plant communities. Isoetids and low-growing plant communities were negatively impacted by increasing amounts of FBOM and DOC, the latter being more pronounced in permanent lakes. At the same time, elevated amounts of organic matter led to an increase of emergent and amphibian plant communities. Stable isotope analysis suggested that the main source of organic matter was allochthonous, possibly resulting from a buildup of organic matter in the catchment of each lake. These results suggest that coastal dune fixation and vegetation encroachment affect plant communities in a similar manner to terrestrial communities, leading to a loss of rare and low-growing dune lake plant species specialists and a favoring of more common and competitive species.