Perai river is one of the important rivers to Penang and Kedah states. Many industries are located along the river that flows to the Strait of Malacca. In order to gather the status of pollution along the river, a total of 47 stations were established to measure the heavy metals content and the sediment characteristics. Findings show that finer sediments had dominated all sampling sites as samples are mostly muddy sediment. The heavy metal concentration in the surficial sediment was analyzed using the Inductively Coupled Plasma Mass Spectrometer after the Teflon Bomb digestion method. The average concentration for Zn, Cr, Cu, Cd, Pb were 74.7±33.3, 66.0±28.1, 21.8±9.05, 0.42±0.32, and 28.6±6.84 μg/g dry weights, respectively. Generally, the concentration of metals studied seemed to be controlled by natural processes. This is proved by the enrichment factor, categorized as a deficiency to minimal enrichment, and can be concluded to be the main source from the lithogenous in origin. The sources of the heavy metals in some of the stations in the Perai river are speculated from the nearby urban runoff, industry activities along with the river, fishing and shipping activities, and land transportation emission may also accumulate for the pollution in the river.