Altogether, 62 taxa of macrophytes including 18 bryophytes and 16 macro-algal growths were determined at 87 survey sites (73 rivers) representing the both ecoregions in Slovakia (Pannonian and Carpathian) during the years 2010–2013. Bryophytes represented the dominant community in the Carpathians, while the occurrence of macro-algal growths was relatively balanced in both ecoregions. Ordination analyses (DCA) showed an obvious shift within studied survey sites from vascular plants to bryophytes, while macro-algal growths were more or less uniform distributed in the whole ordination space. Based on stepwise (forward) selection in CCA, altitude and water surfaces as a land use type were the main environmental factors responsible for this pattern and explained 13.7% of the variability. Variation partitioning showed that the shares of environmental variables on the total variation decreased in the following order: both groups together 8.3% (landscape and geographical variables, physicochemical variables), followed by landscape and geographical variables (5.8%) and purely physicochemical variables which had an insignificant effect on macrophyte composition. The importance of both groups (bryophytes and macro-algal growths) in ecological assessment was also confirmed by their contribution to the mean IBMR value determined for each water body type. Anyway, our study showed that their contribution to ecological assessment is not focused only on small mountain streams where they are dominant. They may obviously affect ecological assessment also in many water body types in lowland rivers and large upland rivers as well.