Since Princeton Ocean Model (POM) has been opened to the public, many researchers in US and recently in Japan use it to many three-dimensional phenomena in environmental problems. The model is characterized by sigma-coordinate system, mode-splitting and 2.5 level turbulence model. Its adaptability, however, has not discussed sufficiently for the stratified flow system. In the present study, POM is applied to simulate the 3-D baroclinic residual flow currents in Osaka Bay and Tokyo Bay, where have many field data and computation results using Osaka Daigaku Estuaries Model (ODEM). As a result, POM is found to produce extremely less spreading of river plume as compared with ODEM's results. It is because the internal stratified interface can not be taken into account in the sigma transformation. POM is still required for many basic discussions.