The shutdown of drinking water treatment plants (DWTPs) at the Langat River Basin, Malaysia, which provides drinking water to almost one-third population in the basin, is very frequent, especially due to chemical pollution in the river. This study explored the pollution sources in the Langat River based on eight specific water intake points of the respective DWTPs to suggest an integrated river basin management (IRBM). Analysis of Al (250.26 ± 189.24 µg/L), As (1.65 ± 0.93 µg/L), Cd (1.22 ± 0.88 µg/L), Cr (0.47 ± 0.27 µg/L), and Pb (9.99 ± 5.38 µg/L) by ICP-MS following the Chelex® 100 column resin ion exchange method found that the mean concentrations except Al were within the water quality standard of the Ministry of Health (MOH) as well as the Dept. of Environment (DOE) Malaysia. However, the determined water quality index based on physicochemical parameters (2005–2015) at the midstream of Langat River was Class III, which needs substantial treatment before drinking. The linear regression model of Al, As, Cd, and Pb suggests that water quality parameters are significantly influencing the increase or decrease in these metal concentrations. Moreover, the principal component analysis (PCA) and the hierarchical cluster analysis (HCA) also support the regression models that the sources of pollution are both natural and man-made activities, and these pollution sources can be clustered into two categories, i.e., upstream (category 1) and mid to downstream (category 2) in the Langat River. The degraded water quality in the midstream compared to up and downstream of the river is mainly due to human activities apart from the natural weathering of minerals. Therefore, the implementation of policies should be effective at the local level for pollution management, especially via the proactive leadership roles of local government for this transboundary Langat River to benefit from IRBM.