Prolonged persistence of toxic cadmium (Cd), chromium (Cr) and lead (Pb) in the aquatic environment are due to its nonbiodegradable characteristic. A few studies have reported higher concentrations of these metals in the transboundary Langat River, Malaysia. This study determined the spatial and temporal distributions of Cd, Cr and Pb concentrations (2005–2015) in the Langat River along with assessing the status of these metals in the drinking water supply chain at the basin. Water samples were collected once in 2015 from the drinking water supply chain, i.e., from the river, treated water at plants, taps and filtration water at households. Determined mean concentrations of Cd, Cr and Pb by inductively coupled plasma mass spectrometry in the Langat River were within the drinking water quality standard of Malaysia and the WHO, except for the Pb (9.99 ± 1.40 µg/L) concentration, which was at the maximum limit, 10 µg/L. The spatial and temporal distribution of these metals’ concentrations indicate dilution of it downstream, along with the increasing trend in rainfall and water flow, especially during the northeast monsoon. Significant correlation and regression analysis of the Cd, Cr and Pb concentrations also indicate that the sources of this metal pollution are mainly the natural weathering of minerals along with anthropogenic activities in the basin. The determined overall water quality of the Langat River is categorized Class IIA (i.e., clean), which requires conventional treatment before drinking; however, the maximum removal efficiency of these metals by the plants at the basin was about 90.17%. Therefore, the proactive leadership roles of the local authorities will be appropriate to reduce the pollution of this river as well as introducing a two-layer water filtration system at the Langat River Basin to accelerate the achievement of a sustainable drinking water supply.