Every water-course is a complicated system which consists of technical and natural elements. The number of these elements and the connections between them are little-known. The aim of the studies was to evaluate the effect of chosen system elements on the aquatic plant communities on the bottom. Longitudinal profile, bottom width, watercourse depth, substrate, level of bed silting, inclination of the slopes, slope protection and the time from the last interference in watercourse’s bed (regulation, maintenance works) were the chosen system elements. The basis of this paper were field studies, which were carried out in 13 small lowland watercourses in the Lower Silesia during the vegetation season in year 2007. For estimating the results of the studies, the rough sets theory was used. On this basis the hierarchy of the influence of elements of the water-course’s bed on the makrophyten communities was determined. ...