This paper considers optimising methods for wastewater treatment systems. The novelty of this subject is in the introduction of state-of-the-art technologies, such as processes for the biochemical oxidation of organic contaminants, and removal of nitrogen and phosphorus, by intensifying the development of nitrifying, denitrifying and phosphorus-accumulating bacteria. The authors show the efficiency of the new biological purification methods. The scientific novelty lies in the fact that the processes of anaerobic–anoxic–oxide treatment of effluents are intensified by reagent-aided chemical and biological removal of phosphorus. New doses for reagents and their optimal point of introduction have been calculated. The authors show that secondary phosphate contaminants being formed in sludge consolidation tanks and sludge storage reservoirs must be considered. Conditions for the removal of phosphorus during the mechanical dewatering of sludge have been determined. The authors propose using integral dependence to estimate the quality of effluents following biological purification. They also demonstrate an improvement in quality indicators for biologically treated effluents: less than 15 mg/l in biological oxygen demand, less than 10 mg/l in total nitrogen, less than 0·5 mg/l in total phosphorus, thereby meeting recommendations of the Helsinki Convention and contributing to environmental safety in St Petersburg, Russia.