The existence of mangroves produces high resistance to flow which affects water level and current in rivers. For this reason, it is crucial to consider the flow resistance factor associated with mangrove vegetation in river hydrodynamic models. This paper describes the numerical simulation of hydrodynamics of the Brunei River, a tidal river with extensive mangrove intertidal zones using MIKE 21 based on two different model representations of mangroves: 1) a model applying spatial Manning’s m coefficient between cells enclosing mangroves and main river, and 2) a model applying uniform Manning’s m coefficient which indicates the absence of mangroves. The calibration and verification mean absolute error (MAE) results indicate that the model with varying resistance distribution captures satisfactorily the water levels and current patterns of the Brunei River covered with mangroves. Based on these findings, the hydrodynamics are properly understood within the Brunei River and the calibrated model can be coupled with water quality modelling to assess water quality of a river with mangrove forests.