Based on the monthly observation during a hydrological year and available historical data, fluxes, seasonal variations of reactive silica (RSi, RSi=dissolved silicate (DSi)+biogenic silica (BSi)) in the Changjiang River and the Yellow River were analyzed for their long-term changes and their controlling factors. The results showed that the compositions of RSi had a significant difference between the Changjiang River and the Yellow River. During the sampling period, monthly average concentration of DSi in the Yellow River accounted for 74% of that in the Changjiang River, while monthly mean concentations of BSi in the Yellow River was three times higher than that in the Changjiang River. The atomic ratios of BSi/RSi were 0.22 and 0.49 in the Changjiang River and the Yellow River, respectively. The relatively higher BSi concentrations in the Yellow River reflected relatively higher degree of soil erosion and turbidity of the water in comparison with the Changjiang River. High sediment flux originated from the Loess Plateau is the main reason why BSi concentration was relatively higher in the Yellow River than that in the Changjiang River in the sampling period. The shares of RSi among the wet season, normal season and dry season were 5.3:3.1:1.6 and 3.8:3.4:2.8 in the Changjiang River and the Yellow River, respectively. More than half of RSi discharge occurred during the wet season in the Changjiang River. During 1958-2014, the variation of DSi concentration was of primary importance in affecting the change in DSi flux in comparison with the discharge in the Changjiang River, which is mostly caused by climatic change (such as temperature variation). Whereas, the combined effects of runoff and DSi concentrations resulted in the decreasing DSi flux in the Yellow River during 1985-2001. Weathering rate and output of silicon in the river basin are largely affected by climatic change such as the temperature variation, and more studies need to do for comprehensively understanding the specific process.