The ecological problems of the urban ecosystem require a complex study to highlight the paths of evolution in the global aspect. The floristic study of urban ecosystems at the current stage of development of human society determined by the urbanization process, which has intensified since the second half of the 20th century. The terrestrial and aquatic vegetation within the urban ecosystems is subject to a pronounced anthropogenic impact. The taxonomic structure of the flora in these ecosystems differs significantly from the flora outside the urban ecosystem, and the indicator species signal an increased degree of environmental pollution and eutrophication. The data of the study of the chemical composition of the water from the rivers that cross the Bălți urban ecosystem are characterized by increased indices of mineralization and pollution with different compounds that hit the aquatic environment through wastewater from different enterprises. Algae have the role of capturing compounds and including them in the biogenic circuit. Some species have adapted to a higher degree of pollution, and others are disappearing from planktonic communities. The study indicates the presence of a small number of species in the studied sector of the river and among the detected species we identified 17 species of indicator diatoms algae in relation to different factors: environmental pH, salinity, trophicity, saprobity, etc.