This study aims to recommend improvement in environmental pollution permit system after introducing the total water pollution load management system(TWPLMS) to meet the appropriate regional environmental goal considering the carrying capacity of environment. In Korea, the permit of facility discharging pollutants is acquired by applying the proposal to the law describing the permit process and conditions of specific by pollution type, e.g., air, water, waste, hazardous materials, etc. European Union adopted the Integrated Pollution Prevention and Control(IPPC) approach to control the pollution problem and have been prepared the Best Available Technique Reference(BREF) Current permit system is insufficient to motivate the voluntary efforts to reduce the pollution discharge and difficult the cross-media problems in a facility. Moreover, the permanent permit of pollution discharge could not reflect the need of higher environmental quality in both regional and national level. In the view of permittee, there is no room to try to find out the total quantity of pollutants from the whole process and area of a facility. After reviewing the permit process of each law in Korea and the related regulations of foreign countries, we recommend that it is necessary to improve environmental pollution permit system in short and long-term. It is recommended to refer the change of permit conditions of dischargers when the total load of water pollutant by the Acts on River Watershed Management and Community Support to the other affecting acts, for example, Sewerage Act, Act on the Disposal of Sewage, Excreta & Livestock Wastewater, Water Quality Conservation Act, etc.. In the long-term, it is recommended to make a standardized process of permit system applicable to all the polluters on the single media and to investigate how to introduce the concept of IPPC to the whole permit system applicable to a facility discharging pollutants to the multi media.