In subtropical coastal waters around Hong Kong, a well-mixed water body is usually observed after typhoons or strong easterly wind events in summer. A calibrated three-dimensional (3-D) hydrodynamic model for the Pearl River Estuary (Delft3D) was applied to study the physical hydrography of Hong Kong waters and its relationship with wind events in the summer wet season. The general 3-D hydrodynamic circulation and salinity structure in the partially mixed estuary are presented here. The effect of wind on vertical mixing was studied for two representative wind directions (NE and SW) and three wind speeds (5, 7.5, and 10 m/s). The computations show that: (i) in general, in the summer wet season, the river plume moves into the western waters of Hong Kong due to the SW monsoon winds, and the current flow is mainly from W/SW to E/NE in the southern Hong Kong waters; the salinity vertical profile indicates that the water is strongly stratified; (ii) a strong SW wind pushes the river plume into a narrow band and decreases the salinity of the surface water in the estuary and its neighboring region; it may also enhance the mixing in the upper layer of water column, but the whole water body is still stratified; and (iii) a strong NE wind pushes the river plume westward away from Hong Kong waters, and more saline coastal waters enter Hong Kong waters; the water only becomes vertically well mixed after a 10 m/s NE wind blows for 5 d, but wind speeds of 5 and 7.5 m/s do not result in the same extent of mixing. We also examined the role of wind in an episodic storm event in August 2003. The strong SE wind from 23 to 26 August strongly mixed the water column. The moderate to weak NE wind during 16–20 August and the spring tide also contributed to the vertical mixing.