The Ministry of Environment, Ministry of Agriculture, Fishery and Forestry, and Ministry of Construction, Transportation and Maritime Affairs are in charge of livestock manure management. There are national statistics regarding the livestock industry such as the National Pollution Source Survey, Livestock Statistic Survey, and Livestock-breeding Trend Survey. The current statistical data are focused on the scale of livestock breeding and the production of livestock manure using these data, but it is difficult to establish database due to lack of information. In order to plan relevant policies including management of livestock manure, the government established database systems such as the integrated information system of livestock manure, the integrated system of national infectious animal-disease prevention, and the Sae-ol public administrative system. We have tried to suggest improvements for the comprehensive environmental information system of livestock manure management by detecting problems in each level of the livestock manure life-cycle, making use of the existing systems, and considering the electronic transfer system of livestock manure. The services and functions of this comprehensive system include information of livestock farmers, the production, collection, transportation, and treatment of livestock manure, the area of agricultural land used for livestock manure, the report of approval and results on livestock manure products, management of statistical information, management of civil affairs, and relevant mobile application services. The system is made up of three processes: first, establishment of GIS-based management database of livestock manure; second, establishment of a history management system for livestock manure transactions; and third, development of a water quality assessment system.