The use of phytomeliorant plants is one of the promising trends in environmental biotechnology to purify waste water. The study was carried out to understand the phytomeliorative qualities of plants of the indigenous flora of the Turkestan Region under controlled conditions and to develop a method for treating wastewater. It was established that the use of a three-stage treatment of municipal wastewater using phytomeliorant plants: Ceratophуllum demersum L., Potamogeton trichoides Cha. Et Schlecht., Potamogeton pectinatus L., Potamogeton natans L.; Cardamine densiflora N. Gontsch., Sium sizaroideum DC.; Veronica beccabunga L, Veronica anagallis - aquatica L. and Azolla caroliniana Willd for 30 days of the controlled experiment reduces the content of organic and mineral ingredients to the MPC values. A method for phyto-meliorative wastewater treatment of one of the sanatoriums in the south of Kazakhstan was developed and carried out in multi-stage bioponds, where water was purified from mineral and organic compounds by 94.9 ± 8.3 - 98.9 ± 7.8% in 12 days. In this study, first of all, nitrogenous compounds were utilized, then there was an active absorption of mineral ions and residual organic matter by plants. In conclusion, significant purification of wastewater was achieved by using indigenous phytomeliorant plants in much shorter time period.