Flow discharge from the river basin into the sea has severe impacts on the immediate vicinity of river channels, estuaries, and coastal areas. This paper analyzes the features and temporal trends of flow discharge at Pearl River’s three main gauge stations: the Wuzhou, Shijiao, and Boluo gauge stations on the West River, North River, and East River, respectively. The results show no significant trend in annual mean discharge into the sea at the three gauge stations. Changes of monthly mean discharge at the Boluo Gauge Station are evident, and a majority of monthly discharge in the dry season displays significant increasing trends. Furthermore, changes of the extreme discharge are quite evident, with a significant decreasing trend in the annual maximum discharge and a significant increasing trend in the minimum one. The significantly decreasing ratio of the flood discharge to annual discharge at the Boluo Gauge Station indicates that the flow discharge from the East River has increased in the dry season and decreased in the flood season since the construction of dams and reservoirs. At the other two gauge stations, the Wuzhou and Shijiao gauge stations, the seasonal discharge generally does not change perceptibly. Human impacts, especially those pertaining to reservoir and dam construction, appear to be responsible for the seasonal variation of flow discharge. The results indicate that the construction and operation of dams and reservoirs in the East River have a greater influence on flow discharge, which can well explain why the seasonal variation of flow discharge from the East River is more evident. Flow discharge from the river basin into the sea has severe impacts on the immediate vicinity of river channels, estuaries, and coastal areas. This paper analyzes the features and temporal trends of flow discharge at Pearl River’s three main gauge stations: the Wuzhou, Shijiao, and Boluo gauge stations on the West River, North River, and East River, respectively. The results show no significant trend in annual mean discharge into the sea at the three gauge stations. Changes of monthly mean discharge at the Boluo Gauge Station are evident, and a majority of monthly season displays significant significant trends, with a significant decreasing trend in the annual maximum discharge and a significant increasing trend in the minimum one. The significant decreasing ratio of the flood discharge to annual discharge at the Boluo Gauge Station indicates that the flow discharge from the East River has increased the dry season and decreased in the flood season since the construction of dams and reservoirs. At the other two gauge stations, the Wuzhou and Shijiao gauge stations, the seasonal discharge generally does not change perceptibly. Human impacts, especially those pertaining to reservoir and dam construction, appear to be responsible for the seasonal variation of flow discharge. The results indicate that the construction and operation of dams and reservoirs in the East River have a greater influence on flow discharge, which can well explain why the seasonal variation of flow discharge from the East River is more evident.