This study aims to determine the spatial and temporal variation on water quality and to identify the main pollutant sources in Melaka River basin. Based on nine monitored sampling stations, twenty variables of water quality data were used in this study for year 2016. Multivariate statistical techniques include Pearson correlation analysis, principal component analysis (PCA), and cluster analysis (CA) is applied to analyze the water quality data. The results indicate water quality in several stations were over the limit of Malaysian water standards. PCA used to compute the pattern within the analysis of water samples, and recognized on five factors in dry and wet season with the total of variation is 73.22% and 76.58% in the river water data respectively. These suggest concentrations of pollutant sources are associated with point source (municipal and domestic waste, sewage treatment plants, and industrial effluents), non-point source (agriculture, livestock), and natural process (weathering of soil and rock). CA explained rainfalls and other sources including surface runoff and wastewater discharges which become main contamination indicator to relatively affect surface water quality through spatial and seasonal variation. Overall, municipal wastes and industrial effluents required serious treatment due to potential impact on water and potential hazard to consumer’s health. Therefore, this study suggests anthropogenic activities in Melaka River basin required wise management.