Rational use of natural resources implies waste-free production without a negative impact on the environment. Biotechnological methods are often the most effective in solving the problems of waste disposal due to the fact that they are based on natural mechanisms of self-healing in disturbed ecosystems. The aim of the study was to isolate and study the properties of new strains of green microalgae cultivated on residual phosphorus-containing waters, which are promising for the production of biofertilizer. Based on the study of algaeflora from natural reservoirs and wastewater in the south of Kazakhstan, strains of green microalgae Chlorella vulgaris ASLI-1, Chlorella vulgaris ASLI-2, and Oocystis borgei AТР were isolated, capable of consuming phosphate phosphorus and ammonium nitrogen from residual waters in places of storage of solid phosphorus-containing waste.