Aquatic vegetation is a reliable indicator of the ecological condition of surface waters. Abundance, composition and spatial structure of aquatic communities are shaped by an array of factors, which include both natural abiotic features of an ecosystem and external influences. We investigated whether the physical features, i.e., wind exposure and slope of the lake basin, have a significant impact on the taxonomic composition and spatial structure of macrophyte communities from non-impacted, highly alkaline, lowland lakes of the European plains (Poland). We further examined whether these features can affect the classification of the ecological status of lakes assessed in accordance with the Water Framework Directive requirements. Morphological, botanical and physicochemical data from 260 transects in 16 non-disturbed lakes of Polish lowlands surveyed in the years 2011–2016 were analysed. For each transect, littoral slope and wind exposure were calculated. Additionally, the total phosphorus concentration was used as a proxy of water trophy. The relationships between environmental variables and macrophyte indices as well as the syntaxonomic composition of aquatic and rush vegetation (dependent variables) were analysed using multidimensional ordination techniques (redundancy analysis, variation partitioning and indicator values), correlation and regression analysis. Among the three analysed environmental factors (littoral slope, wind exposure and water trophy), in almost all cases the latter explained the highest variance in the macrophyte community, while the contribution of the first two was at most moderate, weak or usually statistically insignificant. However, lakes with steeper slopes were more frequently inhabited by stoneworts and had better ecological status than those with a gentle littoral shape. This may be attributed to the links between lake morphometry and rate of eutrophication, with deep lakes supporting more effective dilution of substances. Furthermore, lower light requirements of charophytes than of higher plants and the capacity to growth in unstable sediments facilitate charophyte establishment in deeper and steeper parts of the littoral over higher plants. Our findings suggest that in lowland lakes with relatively small areas, moderate depths and low wind exposure typical of European plains, slopes and weaving do not hamper vegetation development and do not negatively affect the macrophyte assessment of ecological status. In such ecosystems, eutrophication seems to be a more important factor determining aquatic vegetation than physical features.