Water shortage has been an issue for urbanized areas. For the Penang state in Malaysia, it is forecast that there will be a significant increase in water demand in the future. Penang authorities in Malaysia are trying to find an alternative water source to overcome the problem, with one of the options being the Perai River catchment. However, the river water quality was found to be polluted and not suitable to be used for water extraction for domestic consumption. This paper aims to study the pollution level variation due to changes in rainfall during the year in the Perai River Basin, and estimate the TMDL of the river in a particular case for BOD, COD, and NH3N parameters. A water quality model was developed for the Perai River, Jarak River and Kulim River using InfoWorks ICM. The year 2016 was selected as a model event due to data availability. BOD, COD and NH3N concentrations were used for TMDL calculation, and the load duration curve approach was used to estimate TMDL. The tidal effect at the downstream of the Perai River was found to impact the data analysis in the river stretch. It was found that pollutant load exceedance was the highest during the rainy season and the problematic pollutant was NH3N. Thus, local authorities need to focus on tidal and seasonal change factors when developing action plans to manage water quality issues in this basin.