Anthropogenic activities have had a great impact on the characteristics of watershed pollution. The Pearl River basin is the third largest river in China, but it has been affected by eutrophication impact for a long time. This study comprehensively evaluated the nutrient pollution characteristics of the Pearl River basin from 2016 to 2018. The result shows that the ratio of total nitrogen (TN) and total phosphorus (TP), TN/TP was 24.7 of the Pearl River basin, which indicated that phosphorus was the restrictive factor for eutrophication problems. The limitation of TP maybe caused that TN is difficult to decrease through denitrification and nitrification. The fluxes of TN and TP remained stable in recent 20 years, and the flux of TN and TP transferred from the Pearl River basin to the ocean was 6.86×10⁵ and 2.84×10⁴ t in 2017, respectively. The Pearl River estuary had the largest discharge, accounting for more than 40% of the Pearl River basin. The TN in the West River and North River had a high pollution load, while TP pollution in the East River was very serious. It is necessary to establish an effective mechanism to control nitrogen and phosphorus. A large amount of nitrogen and phosphorus caused the decrease of dissolved oxygen (DO) and the increase of chemical oxygen demand (COD), which aggravated eutrophication. This study of nutrient elements fluxes and distribution in the Pearl River Basin are one of the important prerequisites for clarifying the causes of eutrophication, providing data and theoretical support for further water pollution control and water environmental protection in the future, and also providing a basis for pollution control decisions.