Eutrophication is one of the major environmental problems of the Black Sea, resulting in uncontrolled enrichment of the sea water with nutrients – nitrogen and phosphorus. This autoaccelerating process can be stopped effectively by implementation of advanced technologies for wastewater nutrients removal, some aspects of which are objectives of this paper. The University of Cape Town (UCT) technological scheme was examined in series of experiments with different technological parameters. Completely mixed continuous flow automated reactors were used. The experiments were conducted with real municipal wastewater. The mass fractions and the relevant substrates, utilized by three essential groups of microorganisms (poly-P and nonpoly-P heterotrophic and nitrifying bacteria) were determined. As a result of the derived relationships, based on the simplified procedure developed, the kinetic parameters of these groups of microorganisms were determined, as a base for nitrification-denitrification biological excess phosphorus removal system design and simulation.