Songji lagoon, one of the major lagoons located along the East coast, is considered to be worth preserving because of its good water quality. To consider ways to manage the water quality of Songji lagoon, this study was conducted by employing the analysis technique for system analysis of the water quality model. This study used WASP model which is a model with hydraulic part and water quality part combined. The model for Songji lagoon used the same value as the coefficients of water quality reaction used for Hwajinpo model. And it was revised and verified with the water quality measured in Songji lagoon. The spatial concentration of water quality of Songji lagoon and Hwajin po exhibited different distribution respectively, yet showing a similar characteristic in physical and water side structure. The major water quality items used in system analysis are BOD, limiting nutrients (N, P). The principal conditions reflected the system analysis are an increase or decrease of Allochthonous pollution load and removal of sediment. The study results show that the water quality of Songji lagoon is considerably changed more in sediment than Allochthonous pollution load. Especially, the management of Nonpoint pollution due to a temporary rainfall is more important among allochthonous pollution load.