Using the hydrographic data collected during August 19 to September 12, 2011 and the altimetry data, we studied the characteristics and distribution of water masses in the northern South China Sea (SCS). In this study, fuzzy cluster analysis of temperature and salinity data was employed to categorize the water in the northern SCS vertically in terms of five groups: the coastal mixing water mass (M), the surface water mass (S), the subsurface water mass (U), the intermediate water mass (I), and the deep water mass (D). Results show that there is Kuroshio water intrusion into the SCS in summer 2011, and that the intrusion could reach 119°E. The geostrophic currents derived from the altimetry data show several meso-scale eddies, including two anticyclonic eddies east of Dongsha Island and east of the Luzon Strait, respectively, and a cyclonic eddy south of Dongsha Island. This indicates distinct meso-scale structures of the circulation in the northern SCS in summer 2011, which would influence the vertical distribution of water mass and the Kuroshio intrusion.