Phosphorus was the stoichiometrically limiting nutrient in the Pearl River Estuary (PRE). In order to examine how the river discharge regulates phosphorus dynamics in the PRE, the concentrations of dissolved inorganic phosphorus (DIP) and organic phosphorus (DOP), particulate inorganic phosphorus (PIP) and organic phosphorus (POP) in the water column were determined in May 2015 (spring), August 2015 (summer) and January 2016 (winter). Our results showed that all types of phosphorus were significantly lower in spring and summer than in winter. The Pearl River discharge input played an important role in regulating phosphorus dynamics. Strong vertical mixing in winter resulted in high levels of total particulate phosphorus (1.50 ± 0.97 μM) and dissolved phosphate (DIP: 1.44 ± 0.57 μM, DOP: 0.58 ± 0.42 μM) at the surface. On the other hand, the river discharge input created stratification in spring and summer, favoring the settlement of suspended particulate matter and enhancing light levels. This promoted phytoplankton growth, which was responsible for a DIP drawdown of 0.43 ± 0.37 μM in May and 0.56 ± 0.42 μM in August at the surface. Additionally, stratification restricted the bottom phosphorus replenishment. Our findings provided an insight into processes causing stoichiometric P limitation in the PRE.