The vegetation of the aquatic and marshland habitats of the Orava region (north of Slovakia) was studied in 2009, using traditional phytosociological methods. Sixteen aquatic and eighteen marsh plant communities were described within 96 phytosociological relevés by using TWINSPAN with the application of the dominance principle. Three associations, Potametum alpini, Potametum zizii and Ranunculo-Juncetum bulbosi, were found as new communities for Slovakia. Myriophylletum verticillati, Potametum nodosi, Potametum graminei and Alisma gramineum community were recorded in the northernmost localities in Slovakia. Among marsh communities, Calletum palustris is very rare, both in the Orava region and in Slovakia as a whole. According to Ellenberg's indicator values (EIV), moisture was evaluated as the main ecological gradient. Plant communities are ordered along the first Detrended Correspodence Analysis (DCA) axis in a typical hydroseries (Potametea → Lemnetea → Phragmition communis → Phalaridion arundinaceae, Oenanthion aquaticae and Sparganio-Glycerion → Magnocaricion elatae). The second DCA axis was most correlated with EIV for nutrients. Among the five directly measured ecological characteristics (temperature, pH and conductivity of water, water depth, and substrate type), conductivity of water (0.44, P < 0.01) and substrate type (0.32, P < 0.05) were the statistically significant variables explaining the variability along the first DCA axis.