Based on a hydrodynamic-ecological model, the temperature, salinity, current, phytoplankton (Chla), zooplankton, and nutrient (dissolved inorganic nitrogen, DIN, and dissolved inorganic phosphorous, DIP) distributions in the Beibu Gulf were simulated and the nutrient budget of 2015 was quantitatively analyzed. The simulated results show that interface processes and monsoons significantly influence the ecological processes in the gulf. The concentrations of DIN, DIP, phytoplankton and zooplankton are generally higher in the eastern and northern gulf than that in the western and southern gulf. The key regions affected by ecological processes are the Qiongzhou Strait in winter and autumn and the estuaries along the Guangxi coast and the Red River in summer. In most of the studied domains, biochemical processes contribute more to the nutrient budget than do physical processes, and the DIN and DIP increase over the year. Phytoplankton plays an important role in the nutrient budget; phytoplankton photosynthetic uptake is the nutrient sink, phytoplankton dead cellular release is the largest source of DIN, and phytoplankton respiration is the largest source of DIP. The nutrient flux in the connected sections of the Beibu Gulf and open South China Sea (SCS) inflows from the east and outflows to the south. There are 113709 t of DIN and 5277 t of DIP imported from the open SCS to the gulf year-around.