An comprehensive survey by hydrological, chemical and biological teams in the demonstration Eco- Securaty Zone of Jiulongjiang Estruary was conducted in Xiamen, China(24.3°-25.6° N, 117.7°-118.2° E) during spring(early May), summer(middle August)and autumn(late November)of 2009, aiming to support Eco-Security management of the estuary. This paper studied phytoplankton species composition, abundance, spatial distribution, community structure, seasonal and interannual variation due to the variations of environmental factors in fresh, brackish and sea waters. With analysis results of 97 samples taken from 21 stations in 3 seasons, it showed that there were 135 species of 7 phyla recorded. Diatom was the dominant species in abundance. Chlorophyceae was subdominant though it was dominant in freshwaters. Dinophyceae and Cyanophyceae were seldom observed and Euglenophyceae and Chrysophyceae even rarely in contrast to Xanthophyceae which was common in 3 seasons. Composition of phytoplankton species varied spatially. The phytoplankton, according to its ecotype and habitat can be grouped into freshwater, coastal and eurysalinity and oceanic species. The most important species in brackish and sea waters were Skeletonema costatum, Eucampia zodiacus, Coscinodiscus spp. Melosira granulate, Cyclotella caspia and etc.. The freshwaters were predominated by Planktosphneria gelotinosa, Scenedesmus spp., Pediastrum spp., Phormidium tenus and etc.. In contrast to a remarkable seasonal and spatial variation of species composition, the phytoplankton abundance changed less with stations horizontall though it varied with seasons. The abundance of phytoplankton ranged from (12.10-1135.21)×10³cells/L with means of 116.16×10³cells/L. Seasonal variation of abundance reached as high as 358.68×10³cells/L in summer, and to the lowest at 39.84×10³cells/L in autumn. It is evedent that distribution pattern and seasonal variation of phytoplankton abundance and was controlled by dominant species. Two areas with high abundance of phytoplankton can be discriminated at brackish wasters and sea waters in the Jiulongjiang Estuary, this 2 high phytoplankton abundance areas were supposedly caused by high nutrient input and interaction of interface generally. The Shannon-Wiener diversity indices and Pielou's evenness of phytoplankton community were low in brackish waters with sharp seasonal change. High abundance of Skeletonema costatum and Eucampia zodiacus were the cause of lower diversity, heterogeneous distribution and community simplification. Compared with historic dada composition of phytoplankton species became much diversified jointed by freshwater algae though abundance was lower than it used to be. Though the community were obviously dominated by small and chain forming species, such as Cyclotella caspia and Melosira granulate. It was Skeletonema costatum that remained the most dominant though the Mcnaughton index(Y)reduced sharply. The regression analysis showed that linear correlation, compound linear correlation and multi-regression were significant between phytoplankton abundance and salinity, SiO^-₄, NO^-₃ and PO^3-₄, respectively. Spatial and temporal variation of phytoplankton was associated mainly by salinity and nutrients in the three seasons of 2009. In conclusion, the phytoplankton community in the Jiulongjiang Estuary have made up an unique estuarine biota characteried by significant seasonal variation and hydrologic influence.