The concept of urban ecological health has increased concern over the ecological health of urban rivers. Therefore, in order to study the spatial and temporal distribution of phytoplankton communities and the water quality of Nansha's rivers, Pearl River estuary, eight sites were sampled on a monthly basis from March 2015 to February 2016. During this period, 164 phytoplankton species, from 7 phyla and 73 genera, were recorded. The most diverse group was the green algae (79 spp., 33 genera), which accounted for 48.17% of the total recorded species, followed by diatoms (41 spp., 17 genera), which accounted for 25% of the total recorded species, and the dominant species included Cyclotella meneghiniana, Pseudanabaena sp., and Chlorella vulgaris. The overall abundance ranged from 0.19×10⁶ to 101.34×10⁶ cells/L and exhibited a unimodal pattern of seasonal variation. The peak abundance corresponded to an algal bloom that occurred in April 2015, during which the dominant species, Schroederia nitzschioides, reached 87.38×10⁶ cells/L at site 14 (S14) and then rapidly decreased over the next month. The seasonal succession of the phytoplankton community structure in Nansha's rivers conformed to the Plankton Ecology Group (PEG) Model, with Chlorophyta dominating during the spring and summer, Cyanophyta dominating during the end of summer and autumn, and Bacillariophyta dominating during the winter. The temporal variation of phytoplankton density was significant (P < 0.01), as was the positive correlation of the proportion of Chlorophyta cells in total phytoplankton abundance (r=0.454, P < 0.01). The Shannon-Wiener diversity, Margalef abundance, Pielou evenness, and trophic state indices indicated that Nansha's rivers were experiencing moderate eutrophication. Cluster analysis indicated that the phytoplankton communities possessed high temporal heterogeneity but low spatial heterogeneity. Human activities maybe the key factor for spatial differences. Meanwhile, redundancy analysis (RDA) indicated that chlorophyll a, salinity, dissolved oxygen, water temperature, total nitrogen, and pH were most closely related to the phytoplankton community structure, and pH significantly affected the abundance and species of Bacillariophyta, with alkaline environments benefiting Melosira, in particular. Salinity, water temperature, and total nitrogen were the driving factors of the spring algal bloom.