Abstract: Based on the unstructured meshes and uses finite volume method,an adjoint model of data assimilation is established to study the variation of Bottom Friction Coefficients (BFCs) in tidal bore affected estuaries and to inversely estimate the spatial and temporal variation of BFCs during flood or ebb tide.A series of twin experiments on the BFCs were carried out in a generalized estuary.The experiment indicates that the existence of large spatial variation in BFCs will have a negative effect on the inversed result.The result can be improved with the increase in assimilated observations.The adjoint model is tested using the observed data in the Qiantang Estuary.The derived BFCs during the flood and ebb tide are 0.000149 and 0.001520 (equivalent to 0.012206 and 0.038987 of Manning coefficients),respectively.Both deformation of tidal waves and occurrence of tide bores are successfully simulated using the inversed values of BFCs.The result reconfirms the previous findings that the BFCs during the flood are smaller than that during the ebb in the Qiantang Estuary.