This study proposes a new depth-averaged two-dimensional convection-dispersion model to investigate the seawater intrusion in well-mixed estuary. The new model considers both barotropic salinity flux and the baroclinic flux caused by weak salinity stratification. Liner salinity profile was assumed and physically meaningful baroclinic flux model was constructed base on hydrodynamic consideration. Then, model verification was carried out by simulating seawater intrusion in Takase River. In the new model, the salinity front arrived earlier and the peak value became stronger, which agrees better with the field data measured at Takase Bridge.