A total of 20 water and 17 river bank soil samples were collected from 10 different stations along Malacca River Basin to evaluate the spatio-temporal variations of heavy metals concentration during Southwest Monsoon (SWM) and Inter-monsoon season. Physico-chemical properties of water and soil were conducted to investigate the influence on heavy metals concentration. Inductively Coupled Plasma-Optical Emission Spectrometry (ICP-OES) was used to determine the concentration of target heavy metals (Al, Ba, Cr, Cu, Fe, Mg, Mn, Ni, Sr and Zn) in water and river bank soil samples.The results suggested that heavy metals concentration in water during SWM season was in the sequence of Al> Mg> Fe> Mn> Sr> Cu> Ni> Zn> Ba> Cr whereas for inter-monsoon season, it followed the order of Mg> Al> Fe> Sr> Mn> Cu> Ba> Zn> Ni> Cr. The concentration of heavy metals in river bank soil during SWM season followed the order of Al> Fe> Mg> Mn> Ba> Zn> Cr> Cu> Ni> Sr whereas during inter-monsoon the sequence was as followed: Al> Fe>Mg> Mn>Zn> Cu> Ba> Cr> Ni >Sr. Both the heavy metals in water and soil samples along Malacca River Basin showed almost similar trend demonstrating the pollutants were derived from the same origin. The total concentration of heavy metals during SWM season in present study was lower than that of inter-monsoon season. The spatial metal analyses revealed that downstream stations accumulating metals at significant level than upstream stations due to the influx of pollutants from intense activities in the downstream of the river. Present study is important for providing baseline data for the potential hazardous level of heavy metals to human health, environment, and the sustainable resource management for economically importance of Malacca as a UNESCO World Heritage Site as well as tourist destination.