When the water exchange or substance cycle in inner bays is considered, the permanent current flowing in one direction for longer time, which is composed of tidal residual current, density current, and wind driven current, is more important than the oscillatory tidal current whose magnitude is usually larger. In this paper, a multi-level model was applied to the calculation of permanent current and density variation in Tokyo bay and the change of the state of stratification and the accompanying current field from summer to autumn was simulated. In the numerical simulation, the observed field data such as wind, atmospheric temperature, etc. were used for input of the calculation and the results were compared with the observation values of currents, salinity and temperature. The simulation could describe the reactions of current and density field against the changing wind under the stratified condition pretty well. The long term variations of the vertical structure of salinity and temperature from summer to autumn were also predicted well qualitatively. Additionally, the effects of boundary conditions on the results of numerical simulations were also examined, It is clarified that the simulation results are much affected by the boundary conditions such as river discharge and the vertical structure of salinity at the outer ocean.