Problem statement:The aim of the study was to model the discharge, Biochemical and Chemical Oxygen Demands (BOD and COD) loads in each cross section of Bertam River in Cameron Highlands, Malaysia. Cameron Highlands form the headwater catchment for two major rivers of the lowlands; Pahang River and Perak River. On the other hand, Cameron Highlands is undergoing rapid development as a popular tourist destination and an area exploited for growing of temperature vegetables, fruits and flowers. It is also a mountainous area subjected to torrential tropical showers. The condition of Bertam River as one of the main rivers in Cameron Highlands has degraded over the years in terms of water pollution and river environment. Approach: Therefore, MIKE 11 a onedimensional hydrodynamic simulation program was utilized to model stream flow transport and water quality processing in the river system. The model was used to generate the river outflow and simulate BOD and COD concentrations in each cross section of Bertam River. Hydrodynamic Module (HD) which uses an implicit, finite difference solver was applied to calculate water level and flow for the river. Next, Rainfall-Runoff Module (RR) which is include unit hydrograph method and lumped conceptual continuous hydrological model was used to combine the meteorological data of the study area to MIKE 11 simulation system. Finally, Advection-Dispersion Module (AD) was used for transported BOD and COD concentrations calculation. Results: Water quality results show the BOD 5 varies from 1-2 mg L −1 during pre-monsoon and from 4-10 mg L −1 during post-monsoon. The COD between 39-49 mg L −1 was observed during High Water Flow (HWF). Much lower concentration was detected during Average Water Flow (AWF) which was between 10-14 mg L −1 . The comparative analysis between measured and simulated data showed that MIKE 11 is able to predict sufficiently accurate BOD and COD loads at the catchment outlet especially during AWF. Conclusion: Due to higher discharge during HWF some differences between measured and predicted values were observed. Therefore, it is suggested that for better agreement at higher discharges the hydraulic model simulation to be conducted using more measured flow data and by application of more precise differential equation such as RKQC and RK4.