Abstract: Based on the samples collected in Nansha area in spring, 2013, we investigated the net phytoplankton community in order to determine the effects of water masses on their distribution. A total of 222 species, belonging to 62 genera of 4 phyla, were identified. Bacillariophyta and Pyrrophyta accounted for 67.1% and 31.1% in species number, respectively. The average abundance of net phytoplankton was (16 655±36 570) cell · m^-3. Bacillariophyta accounted for 93.6% in abundance. The average diversity index and evenness index of net phytoplankton were 4.43 and 0.85. The species number and abundance of net phytoplankton were the highest in the mixed waters in the west of Balabac Strait, characterized by shallow thermocline and high nutrient concentrations resulting from the intrusion of Sulu Sea waters and the appearance of a clod eddy. In the mixed waters in the north edge of the Sunda Shelf, the abundance of net phytoplankton was sub-high due to the influence of upwelling. In the mixed waters from coast of the Indo-China Peninsula with low inorganic nitrogen, the species number and abundance of net phytoplankton were low, but the percentage of Cyanophyta increased to the maximum. In the Nansha central surface waters with less terrigenous matter, deep and thin thermocline, the lowest silicate concentration occurred at 0~75 m, the average abundance of net phytoplankton was low, but the percentage of Pyrrophyta increased to the maximum, and the average evenness index of net phytoplankton was the highest, while the lowest abundance of net phytoplankton appeared in the warm eddies.