The Pearl River Delta (PRD) in Guangdong province is one of the most prosperous areas of China. At the same time, a large increase in the production of domestic and industrial waste occurred because of this economic development, and a 10% increase in waste production is estimated to have occurred in the past few years. The complicated river delta system, characterized as criss-cross and multiple river channels, is the primary location at which the Pearl River reaches the South China Sea. Many studies have focused on physical and chemical factors functioning in this region, especially in recent years, but few have investigated their effects on aquatic organisms. To understand the temporal and spatial distribution patterns of Euglenophyta, a riverine phytoplankton community, seasonal investigations were carried out in the river delta area in 2012. Thirteen representative sampling sites settled cover almost the whole river delta area. The correlation between the species richness and the biomass of each genus, and environmental factors is also analyzed in order to identify the key components of the interaction mechanism, using the PCA method. Moreover, the regional characteristics of the phytoplankton biodiversity pattern were evaluated at the genus level, using these results. During the investigation, 84 taxonomic species (including variant and derivative) from 12 genera of Euglenophyta were identified. The high biodiversity in this area is the result of its characteristic geographic features and high rate of eutrophication due to human activities. Of all the genera of Euglenophyta, Euglena contributed most to species richness and biomass, followed by Phacus and Trachelomonas. Although euglenoids in rivers are mainly dependent on exterior supplements from the influx of lentic waters into the river ecosystems, the present results revealed that euglenoids could grow along the river flows. Seasonal variation patterns of species richness and biomass were high in wet seasons and low in dry seasons. Besides the exterior supplementation by water flows during flood periods, simultaneous augmentation of organisms by flows could also promote the growth of euglenoids. Moreover, the corresponding high temperatures present during flood periods also benefit the growth of euglenoids. The spatial distribution pattern of euglenoids showed apparent seasonal differences. During flood periods, the values of the outer sites were significantly higher than those of inner sites, a dynamic mainly associated with variations in flow conditions. In drought periods, the differences among the rural sites were not so significant, but the extremely high values in urban sites were the result of high nutrient influx. The contribution of different genera indicated that Phacus and Trachelomonas could only co-dominate with Euglena during drought periods, and exhibited the K-selection strategy, which is generally characterized by a slower nutrient gathering capacity. In addition, the relationship between the biomass and species richness of euglenoids was analyzed, and it had an incline to the ascending curve part of the unimodal function of global phytoplankton biodiversity patterns.