The bioindication role of macropytes in the assessment of the environmental conditions of small water bodies under the conditions of a megalopolis is discussed. A comparative characteristic is given to the significance of macrophytes from different ecological groups, including hygrophytes (cattail, reed), hydrophyte (pondweed), and hydatophytes (Canada water weed, hornweed), growing in small water bodies in St. Petersburg, for the biogeochemical indication of environmental pollution by microelements (Fe, Mn, Zn, Cu, Cr, Ni, Pb, and Cd) and biogenic elements (K, Ca, Na, P, S). Possible mechanisms of detoxication of heavy metal ions in macrophyte organisms and their role in the stable functioning of water bodies in urban territory under the conditions of anthropogenic pollution are discussed. The prospects of the use of macrophyte groups for the bioindication of pollution and phytoremediation of aquatic ecosystems are analyzed.