The dynamic nature of a river channel entrance is commonly seasonal dependant. This is evidenced in the topography of river channel entrances in East Coast of Borneo which is influenced by both North East (NE) and South West (SW) monsoons on top of surrounding parameters such as waves and tides, sedimentation as well as climate change. Advanced numerical modelling technique is frequently used as a leading approach to investigate the complicated nature of river channel entrance to well represent actual conditions of a designated area. This paper presented a mesoscale numerical modelling method by integrating reductionist and reduced complexity model approach along with local seasonal conditions to well represent river channel entrance problem and propose management measures. The model was established with a set of numerical equilibrium equations and calibrated parameters to reflect the features of regional conditions with the combination of local validated modelling parameters. The model had accurately represented the effects of both NE and SW monsoons in terms of hydraulics and sediment dynamics at the Petagas river channel entrance, as verified by site data and satellite imagery. In addition, the accuracy of the model provides confidence in the implementation of improvement measures at the river channel entrance. The improvement scheme includes a training channel and a breakwater in improving flushing capacity, thus preventing sedimentation and upstream flooding, allowing proper navigation through the river. In conclusion, the accurate investigational result from this numerical model had successfully demonstrated its scientific role in solving dynamic river channel entrance, which can serve as a numerical modelling approach for solving similar river channel entrance problems especially in the East Coast of Borneo with predominant inter-annual seasonal variations.