The Sequential Importance Resampling method is introduced to a two dimensional hydraulic model to estimate inflow and Manning roughness coefficient (Manning's n) simultaneously. The equifinality problem between the Manning's n and the inflow is considered using the proposed method. To solve the problem, we introduce the variance reduction factor and the correction factor in the perturbation step of the proposed method. The perturbed inflow and Manning's n were updated according to the observed water stage with state variables. The result of the proposed method shows good agreement with the observed discharge, which enabled us to estimate the Manning's n and inflow discharge at the same time considering the uncertainties of the existing rating curve. Finally, it showed that the methodology not only estimates the appropriate Manning's n but also improves the existing rating curve.