Vegetation in the river Danube was studied in 1972–2001 to document the changes associated with the construction of a water reservoir. Before 1993, only a single species of aquatic plant, Potamogeton pectinatus, was known to occur in the main channel of the river Danube, which forms the frontier between Slovakia and Hungary. In the 1980s the building of the Gabčíkovo hydroelectric power station started and was finished in 1993. At present, five different aquatic habitats occur in the study area. (i) In the upper part of the Čunovo reservoir, there are stands of reed; Zannichellia palustris and Elodea nuttallii were the first other macrophytes to colonize this area where there are now 11 species. (ii) The Old Danube consists of shallows and margins of the original riverbed, which since 1992 (1851–1811 river km) were occupied predominantly by Zannichellia palustris. The adjacent pools were colonized by Elodea nuttallii, Potamogeton species, Batrachium trichophyllum, Ceratophyllum demersum and Lemnaceae species, and Phalaris arundinacea dominates the littoral areas. (ii) The bypass canal harbours only the moss Cinclidotus riparius growing on the boulders. (iv) Two seepage canals were rapidly overgrown by macrophytes, many species of which were threatened species in Slovakia (Apium repens, Groenlandia densa, Hippuris vulgaris, Chara species). (v) Succession occurred in river arms on the left bank after the damming of the river which resulted in changes in spatial distribution and species composition of macrophytes; a North- American alien species Elodea nuttallii spread rapidly there.