The study presents an attempt of determination of the hierarchy of stream bed system elements, which are shaped by regulatory and preservation works creating qualitative and quantitative composition of aquatic macrophytes communities. The field study was conducted on 29 small and medium lowland streams in Lower Silesia region. One hundred of research sections were chosen on these streams. The study included measurements and description of selected elements of complex stream bed system, such as: longitudinal profile, bottom width, watercourse depth, bank slope, type of bank protection, type of bottom substrate, number of aquatic plants species and bottom coverage with the plants. Rough set theory was used in order to determine the hierarchy of discussed elements interactions on qualitative and quantitative composition of vascular aquatic plants communities. Its application allowed to determine the sequence of interactions of single elements of discussed stream bed system elements, these elements pairs, as well as sets composed of three or four elements, on the number of aquatic macrophytes species observed in the stream and on degree the bottom coverage by them.