We numerically studied saline intrusion and the related river flows in the Abashiri River Estuary that connects the Ohotsuku Sea and the Lake Abashiri in northeast Hokkaido. A three-dimensional object-oriented hydrodynamic model, Fantom3D, was used to investigate the stratified flow dynamics in this estuary. In the computation, the estuary was decomposed into 15 domain objects having different sizes to properly express the narrow and highly bending river channel. The one-way nesting technique was also used to resolve depth-scale eddies in the channel. The computed results were compared to observed data obtained in Sept 2006. The water level, velocity and salinity measured at four locations along the estuary were in reasonable agreement with the computed results. The secondary flow at a bending section and the variation of mixing type along the river were also discussed using the computed results. We showed that these computed results are qualitatively agreed well with the previous investigations.