A Sino–German cooperative project (AMBOS/AMREB) was carried out to improve the understanding of the nutrient–phytoplankton dynamics with processes and governing factors through observation and modelling. Two cruises in April/May 1999, September 1998 and two 15-month coastal monitoring stations were completed and a three-dimensional model for the nutrients–phytoplankton cycle was established. During the cruises in spring and autumn, increased phytoplankton concentrations were found in the southern Bohai Sea characterized by high biomass in spring and higher production in autumn. The annual cycle of nutrients and chlorophyll a concentrations was monitored at Changdao and Penglai. A sudden depletion of nutrients occurs after spring bloom and is replenished by river discharges from summer to autumn and mixing up from bottom in winter. The concentrations in coastal areas were higher than that in the Central Bohai Sea. The Laizhou Bay and the Central Bohai Sea had the maximum annual mean biomass and primary production, while the Bohai Bay had the lowest values. The Huanghe River, the most turbid one in the world, with large sediment load enters the Bohai Sea and causes the low transparency around its mouth especially during strong wind mixing time. This influences the annual cycle of phytoplankton significantly in that area. Comparing with the historical data of 1982/1983, 1984/1985 and 1992/1993, the annual cycle and horizontal distribution pattern did not change much within two decades. Diatoms and dinoflagellates are the major components of the phytoplankton community in the Bohai Sea and the ecotype of these phytoplankters is temperate and neritic. Nanophytoplankton is a major component and the picophytoplankton is also not negligible. In spring, the phytoplankton community is mainly composed of small cell diatoms and in autumn of big cell diatoms and dinoflagellates. The replacement of diatoms by dinoflagellates is the main feature of phytoplankton changes in recent years. Using DIN, phosphate, phytoplankton and bottom detritus biomass as state variables, a three-dimensional ecosystem model (ECOHAM) is established coupled with the hydrodynamic model (HAMSOM). The simulation was carried out for the year 1982 because hydrodynamic model simulations and meteorological data were available. The simulated nutrients (dissolved inorganic nitrogen [DIN], phosphate), phytoplankton biomass and primary production variability are in reasonable agreement with the observations. Using model results of 1982, the phytoplankton processes could be discussed by model sensitivity studies. The variation of the phytoplankton was controlled by temperature, nutrient and especially by available light, which was strongly influenced by transparency. The annual phytoplankton cycle was sensitive to the basic respiration rate, mortality rate and grazing rate and to the limitation of light. The net primary production of phytoplankton is 7469 kt C. Respiration of phytoplankton take great role in the regeneration of nutrients and it can compensate 62% of the nutrients consumed by algal growth while bottom remineralization, another important source for nutrients regeneration, can add 23%. The influences of horizontal advection, river loads and different biological processes are also discussed based on this model simulation. The maximum of biomass without horizontal advection in summer is two times higher than that with advection and the high biomass area locates along the shore. Transported by horizontal advection, the high biomass area extends to the east in the Laizhou Bay, to the southeast in the Liaodong Bay and concentrates at north in the Bohai Bay. The variation of the river load only has regional influences to the evolution of the system. The increasing of the proliferation of industries, agriculture and domestic sewage compensates the drop of the DIN concentration induced by river load shutdown. If only the phosphorous cycle is considered, the simulated biomass is six times higher and the situation of the Bohai Sea cannot be adequately reproduced.