In the Pearl River Estuary (PRE), the bottom hypoxia has occurred in summer since 1990s, which resulted from phytoplankton bloom fueled by riverine discharge of bioavailable nutrients. In July of 2017, we observed the largest bottom hypoxia (approximately 1,700 km2) that has been reported ever, spanning from Huangmaohai to Hong Kong Island. From the biological parameters we measured during the cruise, we suggest that the mechanism underlying the formation of the bottom hypoxia and the phase of its development were spatially heterogeneous. In the western area near Huangmaohai, widespread high chlorophyll a concentration > 10 μg L−1 was observed in the surface water. In contrast, primary production was generally low in this area and high only near the river mouths, where the detectable phosphate remained at surface. These observations suggest that additional supply of nutrients, particularly phosphate, from Huangmaohai and western tributaries of the Pearl River fueled primary production in this area. On the contrary, the eastern area near Hong Kong Island was characterized by low chlorophyll a concentration and primary production, and high bacterial abundance and production. These observations suggest that the phytoplankton bloom in this area had reached a decline phase and regeneration production had prevailed. High abundance of Synechococcus and the detectable level of ammonium at surface also support this explanation. The present results revealed the importance of nutrient load from Huangmaohai in expansion of phytoplankton bloom and subsequent bottom hypoxia in the PRE.