<p><i>Coleanthus subtilis</i> is a globally rare therophyte growing on exposed bottoms of water reservoirs and riverbanks, where it forms dense patches, while specimens differ morphologically within the population. However, factors determining its morphological variability and habitat features favoring its good performance remain poorly understood. Also, despite the fact that it is threatened in many regions, it shows a potential to conquer new localities, especially anthropogenic habitats, and dominate in some phytocoenoses. Therefore, we analyzed in detail the main morphological features of the species in relation to bottom sediment characteristics, i.e. pH and macroelement content and ecological preferences, illustrated by the values of ecological indicators, and phytocoenoses composition. We showed that pH, N and P content, as well as the moisture of the bottom sediments determine the intrapopulational morphological variability of <i>C. subtilis</i>. Different morphotypes can co-occur in one vegetation patch, but one morphological type usually prevails depending on bottom sediment characteristics, and the coverage of individuals of other plant species, as well as the <i>C. subtilis</i> itself. Our results show the link between <i>C. subtilis</i> morphotypes and habitat parameters, and shed light on the relationship between its morphotypes and the coverage of individuals of various species comprising vegetation patches, which can be considered in management and conservation of this species.</p>