Carbon (C) and silicon (Si) biogeochemical cycles are important factors in the regulation of atmospheric CO2 concentrations and hence climate change. Theoretically, these elements are linked by chemical weathering and organism stoichiometry, but this coupling has not been investigated in freshwaters. Here we compiled data from global rivers and lakes in the United States of America and the United Kingdom, in order to characterize the stoichiometry between the biogeochemical cycles of C and Si. In rivers this coupling is confirmed by a significant relationship between HCO3-/Na+ and DSi/Na+, and DSi:HCO3- ratio can reflect the mineral source of chemical weathering. In lakes, however, these characteristic ratios of chemical weathering are altered by algal activity. The lacustrine Si:C atomic ratio is negative feedback regulation by phytoplankton, which may result in this ratio in algal assemblages similar to that in water column. And this regulation suggests lacustrine photosynthetic C fixation in this equilibrium state is quantitative and depends on the DSi concentration. These findings provide new insights into the role of freshwaters in global C and Si biogeochemical cycles.