The Pearl River Delta (PRD) in Guangdong province is one of the most economically prosperous areas in China. Economic development in this region has resulted in an estimated 10% increase in the volume of domestic and industrial wastes in the past few years. The complex river web of the delta, characterized by multiple river channels, forms the entrance for the Pearl River into the South China Sea. A number of studies have focused on measuring the physical and chemical factors in this region, but there has been little attention paid to aquatic organisms. Our objective was to document the ecological characteristics of copepods in the river network of the Pearl River Delta. The species composition, biomass, and biodiversity of copepods were measured in samples collected from the water in March, May, August, and December of 2012. A total of 31 copepod species representing 24 genera and 9 families were identified, including copepodids and nauplii. The dominant copepod species exhibited seasonal and spatial changes in abundance, with being the most common species. The biomass of copepods and nauplii exhibited seasonal changes in abundance, and both were more abundant during the wet season than in the dry season. The copepod biomass was characterized by even horizontal distribution, whereas the nauplii biomass generally decreased along a gradient from southwest to northeast. In general, the average biodiversity and evenness indices were higher in the wet season than in dry season, and decreased from the southwest to northeast. The results of principal component analysis revealed that the community structure of copepods in the Pearl River Delta river network was significantly positively correlated with temperature, total phosphorus, total nitrogen, ammonia nitrogen, and permanganate contents, positively correlated with chlorophyll acontent, and significantly negatively correlated with water transparency and pH.