Lake water quality assessment information is useful to anyone involved in lake management, from lake owners to lake associations. It provides lake water quality criteria, which can improve the ways how to manage out lake resources and how to measure current conditions. It also provides a knowledge base so that the lakes can be protected and restored. Here, the Freshwater Lake Water Quality Management System(FLAQUM) was developed. The results of FLAQUM application by scenario proved that pollutant load at rainfall by the nonpoint sources was much more than normal times at rainfall. From the result of Scenario I (pollutant source increase case), the concentrations of Boryeong freshwater lake were BOD 9.43mg/L, T-N 4.53 mg/L and T-P 0.21 mg/L, respectively, and those values exceed the standard of agricultural water. And in case of Scenario I and II(the present case) excluding Scenario III (pollutant source decrease case), all of T-N and T-P are either mesotrophication or eutrophication, on the other hand when 60% of pollution source is removed, the concentrations of Scenario III were BOD 3.21 mg/L, T-N 0.95 mg/L, T-P 0.11 mg/L, respectively, and which satisfies the standard of agricultural water quality.