For the Pinang River, originating in the western highlands of Penang Island, the nature, sources and extent of pollution were studied. The river water samples collected at five selected sites were analyzed for various physical and chemical parameters, namely temperature, DO, BOD, COD, SS, pH, ammoniac nitrogen (AN), and conductance, Long-term data of rainfall and temperature were analyzed to determine the seasonal variations of the streamflow. The streamflow during the dry season is extremely low compared to the wet season, thus concentrations of contaminants derived from point pollution source increase due to lack of rainfall and runoff events. On the contrary, in the predominantly urban and agricultural catchments, non-point pollution source increases during rainy season through seepage and runoff. Effects of seasonal variations consequently determine the quantity and quality of the water parameters. The Jelutong River, the Dondang River and the Air Itam River carry the seepage from widely urban and residential areas to the main Pinang River systems. Water quality of the Pinang River at different points assessed by the water quality indices was compared. According to the quality indices during the study period, water quality in the upper reaches of the river is medium to good. It dwindled in the plains, due to the seepage from urban areas and discharges from the industrial and agricultural lands.