The contribution discusses macrophyte communities in natural and man-made waterbodies located on the active floodplain along the Drava river (Slovenia). We presumed that these different types of wetlands host a great number of macrophyte species, but this diversity may be affected by the presence of alien invasive species Elodea canadensis and E. nuttallii. Presence, relative abundance, and growth forms of plant species along with selected environmental parameters were monitored. Correlation analyses and direct gradient analyses were performed to reveal the possible relations between the structure of macrophyte community and environmental parameters. Number of macrophytes in surveyed water bodies varied from 1 to 23. Besides numerous native species we also recorded Elodea canadensis and E. nuttallii, which were present in 19 out of 32 sample sites, with E. nuttallii prevailing. The less invasive E. canadensis was absent from ponds and oxbow lakes but relatively abundant in side-channels, while E. nuttallii was present in all types but dominant in ponds. The most abundant native species were Myriophyllum spicatum and M. verticillatum, Ceratophyllum demersum and Potamogeton natans. Correlation analyses showed no negative effect of the invasive alien Elodea species to the species richness and diversity of native flora. Positive correlation between the abundance of E. nuttallii and temperature of the water was obtained.