The influence of hydrodynamics on the chemical composition of sediments is based on the uneven distribution of element abundances in different size fractions. In this study, 72 size-fractional sediments from the Huanghe (Yellow River) and Changjiang (Yangtze River) riverbeds were measured with XRD, SEM, ICP-AES and ICP-MS. The analysis results show that the mineral and chemical characteristics change with grain size in the Huanghe and Changjiang sediments. According to the principal components analysis, three independent geochemical factors were found. The first factor elements, Zr, Hf, Th, U, Y, La and TiO2 are influenced by the existence of heavy minerals. The second factor elements, Al2O3, alkalis, alkaline earth (excluding Ca and Sr) and most of the transitional metals are dominated by clay minerals. The third factor group includes Ca and Sr, which were controlled by calcium-bearing mineral contents and chemical weathering intensities. The various grain size distributions greatly affect the mineralogical and chemical compositions of bulk sediments. Compared to other size fractions, the 5–6PHI size fractions of the Huanghe and Changjiang sediments have special mineralogical and chemical compositions, and intermediate volume percentages. Weight or volume percentage of each size fraction may be more suitable than mean grain-size of the bulk sediment to elucidate the grain size effects. Chemical Index of Alteration (CIA) values increase steeply with decreasing grain size, while Weathering Index of Parker (WIP) values are relatively stable. Because of the big influence of the abundance of clay minerals on CIA values, it is questionable to use CIA as a proxy of weathering intensity. Considering the clay mineral effects, stability in values and heterogeneous material properties, WIP has the potential to indicate the chemical weathering intensity of sediments. Copyright © 2014 John Wiley & Sons, Ltd.