This study investigates the hydrodynamic variations in the coastal region of Nan-bin, Hualien influence by the topography and water stratification. The data used were collected from four cruises of field observations in 2008/4/29¡B2008/9/5~6¡B2009/3/17~18 and 2009/7/21. Instruments applied include sb-ADCP and CTD. Parameters recorded include flow velocities, water temperature and salinity and tidal elevations. The collected data are analyzed through a variety of time series analysis technique, including buoyancy frequency EOF analysis, potential vorticity and kinetic energy. The results show that (1) the flow field and vorticity in the south side of Hualien Harbor indicate there exist a counterclockwise eddy during flood. The flow pattern reverse to be a clockwise eddy during ebb. The current speed and vorticity is smaller in the surface layer, while the bottom current speed and vorticity is much larger. (2) Currents in transects of along slope, along canyon and along shore all reveal two layers flow separated around 25m, with upper layer flowing eastward and lower layer westward. The current velocity reaches to a maximum at 55m, and the current directions were dominated by the orientation of bottom topography. The baroclinic kinetic energy increase to 0.15m2/s2 along the down slope transect, while the up slope kinetic energy reduced to 0.05m2/s2. (3) The CTD data suggest that the upper layer is warm-fresh water due to river outputs, while the lower layer is dominated by cold-salty open ocean water. (4) The density interface at 25 m is confirmed by buoyance frequency analysis. The EOF analysis of density distribution shows eigenvalue of first mode has maximum at 53m, while the second mode has peaks at 25m and 65m, which match well with the vertical of distribution of flow structures.