Numerical ocean modeling usually composes various initial- and boundary-value problems. It integrates hydrodynamic and thermodynamic equations numerically with atmospheric forcing and boundary conditions (lateral and vertical) from initial states of temperature, salinity and velocity. Past observations, historical datasets and climatological datasets of the ocean have contributed greatly to the knowledge of the data fields of initial condition, atmospheric forcing and boundary conditions. Change in either initial or boundary condition leads to a variety of model solutions. It is necessary to specify realistic initial and boundary conditions to achieve better understanding and prediction of the ocean behavior. However, uncertainty often exists in both initial and boundary conditions. Up to now, most studies on ocean predictability have usually been for one particular type of model input uncertainty within the three types of uncertainty (initial conditions, open boundary conditions, atmospheric forcing function). This thesis investigates the response of ocean model to the three types of model input uncertainty simultaneously using Princeton Ocean Model (POM) implemented for the Japan/East Sea (JES).