A rainfall event is an important factor that can greatly affect the water quality of a river, particularly in a tropical country where the seasonal variations of river water quality are mainly dominated by precipitation. Hence, the present study aimed to determine the changes in the physicochemical characteristics of the Batang Baram, a tropical river in Malaysia, due to a rainfall event. Two samplings were conducted in the Baram in Sarawak before and after rain. The results show that the mean velocity and mean depth of the river increased substantially after rain. The high volume of surface runoff coupled with the fast-flowing river significantly increased the dissolved oxygen, oxygen saturation, turbidity, chlorophyll a, total sulphide, hydrogen sulphide, and nitrite-nitrogen in the river after rain; whereas the pH, transparency, and organic nitrogen decreased significantly after rain. The water quality index (WQI) in the tributary after rain showed improvement mainly due to an increase in the concentration of dissolved oxygen. On the other hand, the total suspended solids in the main river after rain changed from Class I/II/III to Class III/V due to soil erosion.