To test the hypothesis that species composition and persistence of phytoplankton communities in nutrient rich lowland rivers mainly depended on physical factors, the temporal and spatial patterns of the phytoplankton biomass were studied seasonally in the Pearl River Delta during 2012a. And its correlation with physical and chemical variables was analyzed to evaluate the key factors and then to display the interaction mechanisms. Samples were differentiated by nutrient level using self-organizing map (SOM), and two apparent different water qualities were found in the present finding. One was characterized by worse than level Ⅴ of water quality and mainly composed by Zhujiangqiao、Lianhuashan and Shiqiao where located near Guangzhou city, and the other was characterized by falling between level Ⅱ and Ⅳ of water quality and composed by the other sites. During the investigation, the 383 taxonomic species (including variant and derivative) from 7 groups were identified. The results showed that the diatom (Bacillariophyaceae) and Chlorophytes were most abundant and they were 41.78% and 29.24% to the total numbers, respectively. The Euglenophyta and Cyanobacteria were subsidiary. This structure pattern was similar to that of the downstreams of Xijiang River and other large rivers in the world. 39 dominant species were listed in Table 2, and Aulacoseira was the base member of phytoplankton communities around the studied area, for its domination throughout the whole year. Only 3 species showed both high biomass contribution and high occurrence, and Aulacoseira granulata var. granulata was predominant, and the benthic diatom Melosira varians and lentic green algae Dictyosphaeria cavernosa were indicator species of drought period and flood period respectively. Seasonal distribution patterns of total biomass were high in drought period and low in flood period, which was mainly related to the dilution by water flow and the sedimentation lost accompanied with high transparency. The spatial distribution pattern showed increasing trend from southwest to northeast, which was in accordance with the spatial pattern of nutrient level and the spatial pattern did not show seasonal difference. For the relative contribution of different groups, diatom was predominant and contributing 80.56% to the total biomass, Chlorophytes and Euglenophyta were subsidiary. Diatom seasonally predominated in drought period, but it was challenged by Chlorophytes and Euglenophyta in flood period since their influx into main stream from dead zones, such as reservoirs and shallow waters in the river basins. PCA analysis also showed that Chlorophytes and Euglenophyta were not correlated with nutrients but chemical factors. In addition, seasonal variations of relative contribution in different sites were also influenced by salinity. In conclusion, physical factors, including water flow and transparency, could not only influence the seasonal variations of the total phytoplankton abundance, but also impact the relative contribution of different groups in the community, while chemical factors mainly determined the spatial distribution pattern. In addition, salinity could also affect the communities of several sites.