Abstract: It showed a very complex hydrodynamic process in tidal rivers. For making reasonable fine emergency plan, the scope, time and extent of pollution damage influence of sudden water pollution incident had been analyzed by EFDC model under different hydrological conditions in Shenzhen Estuary. It had put forward a method for accurately analyzing the dominant hydrodynamic factors in sudden water pollution incident in estuary. On this basis, the dominant hydrodynamic factors of pollutant transport and diffusion had been identified out by the spectrum analysis method based on Fourier transform, and UNIANOVA was used to corroborate the result. It suggested that the tidal hydrodynamic process was the main driving factors in Shenzhen River; but variation of pollutant concentration at each monitor cross-sections was closely associated with land runoff in sudden water pollution incident. It showed that runoff was the dominant hydrodynamic factor of pollutant transport for sudden water pollution incident in the tidal river.