An original methodology for justifying standards for permissible discharge (PDS) of pollutants from an organized source of water disposal was proposed. An approach was presented, based on maintaining the water quality class, defined by the value of the specific combinatory water pollution index at the monitoring cross-section after wastewater discharge. The problems arising in the application of the current methodology for calculating the PDS of pollutants were considered, the results of testing the methodology for substantiating threshold concentrations for calculating the PDS of pollutants and data on calculating the PDS of pollutants from an organized source of wastewater disposal of a chemical plant were presented.