Ecological risk has not been identified well enough for the designers and contractors to take any actions for its limitation. It results from the lack of the basis formed to assess its level objectively. The aim of this study was to determine the standards useful in the evaluation of the ecological risk for aquatic plants in rivers, where it is planned to conduct regulatory works. The basis for the analysis were the results of the study performed in 2008–2014 in unmodified and transformed lowland watercourses in Lower Silesia. 41 study sections were analysed in 11 watercourses. 30 sections were located in regulated watercourses, while 11 were in unmodified streams. The research included vascular aquatic plants identification and the degree of the bottom coverage by these plants. As a result of regulatory works qualitative and quantitative changes in aquatic plants communities were observed. The analysis of these changes concerning the range and conditions of works conduction enabled assigning measures to the factors of the considered risk. It served as a basis for describing the risk register and the matrix of risk. The study demonstrated that the most important threats resulting from the river regulation from the point of view of environmental protection are complete shading of watercourse bed, and in some cases, bed widening and deepening, embankments slope of 1: 1, 1: 0, embankments protection with stone material or their concreting.