Macrophytes are one of the important indicators used in assessing the anthropic impact on aquatic ecosystems. The structure of macrophyte communities of two rivers were compared by species composition, dominant species and projective cover using statistical methods. It is shown that the influence of storm runoff on these rivers is manifested in the form of a change in the dominant species composition. Based on the statistical analysis carried out, it can be argued that, despite the peculiarities of the flora composition of each of the rivers, the influence of storm runoffs largely neutralizes this specificity, determining the situation in local areas immediately below the runoff. In the area of the effluent discharge the dominance of individual species and an increase in the area overgrown with macrophytes was observed. In the area of stormwater discharge on the Psel River, species were usually present:Nuphar lutea,Ceratophyllum demersum,Myriophyllum spicatumand on the Bystrica River—Glyceria maxima,Sagitaria sagittiformis,Stuckenia pectinataandPotamogeton crispus. The use of the NMDS method has been found to provide good insight into the structural rearrangements in macrophyte communities affected by runoff from stormwater systems.