Abstract The mineralogical and geochemical compositions of the sediments deposited by rivers have been used extensively to evaluate past chemical weathering and the physical erosion history of drainage basins at different time scales. However, the role of sediment sorting in the mineralogical and geochemical compositions of river sediment needs to be better constrained because it could significantly modify proxies used to evaluate weathering intensity in the past. In this study, major and trace element concentrations and mineralogical compositions were determined on seven different grain-size fractions of riverbed samples taken from the Pahang and Kelantan Rivers in the Malay Peninsula. The main aims are to assess chemical weathering and the fractionation of alkali elements during sediment transportation under tropical climate conditions. Fine sediments (from <2 μm to 4-8 μm) were characterized by higher concentrations of Al2O3, P2O5, V, Sc, and Cs than coarse sediments (from 8-16 μm to 32-63 μm). The presence of heavy minerals, such as zircon and monazite, was found to have critical effects on the concentration of several elements (e.g., Zr and Th), leading to extremely high elemental concentrations in the coarse-sediment fractions. Variations in elemental concentrations with particle sizes are mainly attributed to changes in the mineralogical composition during mineral sorting and weathering. In both rivers, the intensity of chemical weathering increased with decreasing grain sizes. However, the relationship between grain size and chemical weathering trends in the Pahang and Kelantan River basins was different in each case due to differences in plagioclase and K-feldspar concentrations, especially in the coarse-sediment fractions (16-32 μm and 32-63 μm). Kaolinite percentage, illite chemistry index, and illite crystallinity were directly proportional to the chemical index of alteration (CIA), suggesting that these mineralogical parameters are suitable proxies for determining chemical weathering intensity in sediments that have undergone significant changes due to mineral sorting during transportation. The comparison of Rb/K and Cs/K ratios and the CIA suggested that K and Rb mainly derive from primary minerals during the process of chemical weathering, whereas Cs is mainly present in fine weathered particles due to the reabsorption of Cs on clay minerals. Overall, our results highlight the relationship of grain size and mineral assemblages to different states of chemical weathering (and alkali fractionation) in tropical river basin sediments. These relationships need to be considered when using mineralogical and geochemical compositions to reconstruct weathering history in a “source to sink” approach.