In order to understand current conditions of water environment and investigate improvement methods for water quality in an estuary, it is important to clarify characteristics of flow field and circulation of nutrients. Maizuru Bay has complex shape that the northern part with bay mouth (North bay) is quite narrow, and the southern part is separated into West and East bays. Toshima is located at the separation zone. Due to this complex structure, the tidal exchange with the Japan Sea is not always enough, and a deterioration of the water quality in the bay has been concerned. In this study, we investigate characteristics of tidal current and distributions of nutrients (COD, DO, nitrogen and phosphorus) in Maizuru Bay through the numerical analysis based on the baroclinic model and the ecosystem model. The flow field of tidal current and the distributions of temperature, salinity and nutrients are simulated in the case of the summer with density stratification.