Mo isotopic composition in large rivers is very important for understanding global Mo cycle. At present, temporal variation signatures in the δ98/95Mo in large rivers have not been investigated, which hinder a comprehensive understanding on the mechanism for the variations of Mo isotopic compositions in river water. In this study, we report a one-year-long time series (March 2010 to March 2011) of the δ98/95Mo of both the water and suspended particles collected at Guiping, from the middle reaches of the Xijiang River (XJR), and of the water δ98/95Mo from the lower reaches of the Huanghe River (HHR, or Yellow River) collected at Lijin, China. The results indicate that the temporal variations in the concentration and δ98/95Mo of dissolved Mo in the XJR range from 4.32 to 10.5 nmol/L (mean 7.31 nmol/L) and 1.04‰ to 1.31‰ (relative to NIST 3134) (mean 1.20‰), respectively, but that the particulates have a lower δ98/95Mo (-0.18‰ to 0.58‰). Analysis of the suspended particulates and other chemical parameters of the river water suggest that the weathering of silicates and sulfides is the main contributor to the dissolved Mo content in the XJR. Subsequently, the highly efficient preferential trapping of lighter δ98/95Mo by weathering products such as clay minerals, Fe–Mn oxides, and organic materials in soils and saprolites, which are abundant in the tropical catchment, is the key to the heavy Mo isotope signatures in the XJR. Furthermore, it seems that neither Mo-scavenging by suspended particulates during riverine transportation, nor the weathering of sulfates, significantly influence the δ98/95Mo of the XJR water. Cross comparison among the δ98/95Mo in the waters of the three largest rivers in China (the Changjiang (CJR), HHR, and XJR) indicates that the HHR has the highest Mo concentrations, but the lightest δ98/95Mo, the XJR has the lowest Mo concentrations but the heaviest δ98/95Mo, and the values for the CJR are intermediate between those for the other two rivers. This supports the conclusion that the efficiency of the selective trapping of Mo by soils and saprolites is the main factor controlling δ98/95Mo in these large rivers. The tropical/subtropical XJR catchment experiences intense chemical weathering, the semi-arid temperate HHR catchment experiences very little, and the CJR catchment falls somewhere between the two. Such a relationship between water Mo concentrations and δ98/95Mo agrees with previous observations from many large rivers worldwide. It is therefore suggested that chemical weathering on continents is the key to variations in the isotopic composition of Mo in the waters of large rivers.