One of the important ways to prevent permanent environmental pollution is to constantly monitor its quality, which can be performed in several ways. The present bioindication study analyzed the level of diversity and abundance of biofilm microorganism communities, which illustrate the state of the studied aquatic environment, enabling to determine its quality. The impact of stormwater discharge on the receiver at particular points was evaluated on the basis of the reaction of selected microorganisms or their groups to the substances appearing in the watercourse. The study of indicator organisms gives information about the waters of a given body of water without expensive hydrochemical tests and without causing a burden on the environment during the production as well as disposal of reagents that are consumed in many classical physicochemical analyses. On the basis of selected algal species, the Shannon index and McArthur index were calculated, and the effect of storm sewer discharge on the communities of indicator organisms was determined. The best visible impact of storm sewer discharge was seen on the basis of the entire study cycle in relation to the median of the McArthur index.