Statistical comparison has been performed for Terengganu and Kinta River Basins in terms of surface water pollution status using some selected physico-chemical parameters. Surface water quality data were collected from Department of Environment (DOE) Malaysia and subjected to logarithm transformation (log-scaling), column auto scaling and z-standardization to eliminate the effects of measurement units. Results revealed that pH value is higher in Terengganu River Basin compared to Kinta River Basin. Two-way analysis of variance (2-way ANOVA) showed spatial and temporal statistical significant differences (p<0.05). Hierarchical Agglomerated Cluster Analysis (HACA) revealed two major statistical clusters of water quality monitoring group. Chemical oxygen demand (COD) showed higher value in Terengganu than Kinta River Basins while ammonia-nitrogen (NH3-N) revealed higher value in Kinta compared to Terengganu River Basins. The present study, however, makes several noteworthy contributions to the existing knowledge on spatial and temporal variations of surface water quality and is believed to serve as a baseline data for further studies in surface water pollution.