In the present study, the ecosystem-based water quality model was applied to the Pearl River (Zhujiang) Estuary. The model results successfully represent the distribution trend of nutrients and dissolved oxygen both in the horizontal and vertical planes during the flood season, and it shows that the model has taken into consideration the key part of the dynamical, chemical and biological processes existing in the Zhujiang Estuary. The further studies illustrate that nitrogen is in plenty while phosphorus and light limit the phytoplankton biomass in the Zhujiang Estuary during the flood season.