Harmful algal blooms (HABs) have become a severe ecological problem in coastal waters in recent decades. Under the enhanced anthropogenic disturbance, the Eastern Chinese coastal seas (ECCS), including the coastal waters of the Bohai Sea (BS), Yellow Sea and East China Sea, have been suffering environmental changes dramatically during the past 40 years. However, it is not clear how changes in coastal nutrient pollution, hydrodynamics and climate promote the succession of dominant HAB species simultaneously. In this study we used physical criteria (light availability, temperature and salinity) and chemical criteria (strategy of nutrient utilization) to quantify the competitiveness of the primary HAB species in the ECCS, i.e. Skeletonema costatum, Noctiluca scintillans, Prorocentrum donghaiense, Karenia mikimotoi, and Aureococcus anophagefferens. A risk assessment module has been developed and applied to this study based on the physical criteria of the main HAB species. Model result indicated a strong reliability on locating the potential physical habitat of blooms dominated by specific species. Imbalanced nutrient stoichiometry plays a vital role in HAB species succession in the ECCS, especially potential limitation of dissolved inorganic phosphorus. Due to long water residence time, persistence of nutrient imbalance and organic nutrient accumulation induce frequent blooms of Aureococcus anophagefferens in the BS. Observations and experiments have limitations when describing combining processes that influence HAB development, and need to be complemented with advanced mechanistic models for describing the hydrodynamics and biogeochemistry to allow for hindcasting and forecasting HAB risk under changing environmental conditions