Land conversion from natural forests to plantations (e.g., oil palm) in Southeast Asia is one of the most intensive land-use changes occurring worldwide. To clarify the effects of oil palm plantations on water quality, we conducted multipoint river and stream water sampling in peninsular Malaysia at the end of the rainy season over a 3-year period (2013-2015). We measured the major dissolved ions and stable isotope ratios of water (δ2H-H2O and δ18O-H2O) and nitrate (δ15N-NO3- and δ18O-NO3-) in water from the upper streams in mountainous forests to the midstream areas of two major rivers in peninsular Malaysia. The electrical conductivity increased, and the d-excess value (as an index of the degree of evaporation) decreased with increasing distance from the headwaters, suggesting the effect of evaporative enrichment and the addition of pollutants. We separated the sampling points into four groups (G1-G4) through cluster analysis of the water quality data. From the land use/land cover (LULC) classification maps developed from satellite images and local information, we found that G1 and G2 mainly consisted of sampling points in forested areas, while G3 and G4 were located in oil-palm-affected areas. The concentrations of major ions were higher in the oil palm areas, indicating the effects of fertilizer and limestone (i.e., pH adjustment) applications. The dissolved inorganic nitrogen concentration did not differ among the groups, but the dissolved organic carbon, total dissolved nitrogen, and δ15N-NO3- were higher in the oil palm area than in the forested area. Although the nitrogen concentration was low, even in the oil palm area, the significantly higher δ15N-NO3- in the oil palm area indicated substantial denitrification. This implies that denitrification contributed to the lowering of the NO3- concentration in rivers in the oil palm area, in addition to nutrient uptake by oil palm trees.