Though Brunei Darussalam is a small country, it has the highest percentage of energy usage per capita as well as the largest carbon footprints of 22.9 metric tons per capita in the world. High emission followed by extreme rainfall resulting from climate change is likely to create challenges to manage increased river flow causing floods. The number of wet days has increased by 0.16 days per year based on the analysis of last 45 years precipitation data. Over 115 cases of flooding and 105 landslides were reported in the year 2014 alone. The watershed of Brunei River is low-lying and swampy; consist of mangrove areas extending 10 km downstream to the mouth of the Brunei River. The effects of varying water depth and tides create a complex zone, an excellent habitat for various fish species particularly cat fish and tilapia. Thus, recognizing the potential threat from flooding altering the flow pattern, the present research focuses to assess the impacts of climate change of Brunei River’s flow for the next 20 years. A computer-based modeling tool, WEAP is used to simulate the river flow based on the climatic data, land use change and potential growth of industries.