In this work, the concentrations, temporal and spatial distributions and the relationship between biogenic silica (BSi) and primary productivity are discussed on the basis of the geochemistry character of BSi in the water–sediment system of the Wuliangsuhai Lake and Daihai Lake. The results show that the average concentrations of SiO₃^2- and BSi are 3.0 mg/L and 3.5 mg/g in the overlying water and sediments from the Wuliangsuhai Lake, respectively, while they are 1.0 mg/L and 7.5 mg/g, respectively, in the Daihai Lake. It is the uptake and assimilation of diatom phytoplankton which results in the significant difference of the SiO₃^2- concentrations between the two lakes, and the inputs of surface runoff is one of the important factors in impacting the spatial distributions of SiO₃^2- in the overlying water. The spatial distributions of BSi suggest the Si source of the two lakes and indicate the differences of eutrophication types and ancient primary producer between the two lakes. The eutrophication precesses and ancient primary productivity of diatom phytoplankton are reconstructed by applying the geochemistry information of BSi archived in the vertical concentration profiles in the two lake sediments. The geochemistry information of BSi well responds to the paleoenvironment and paleoclimate of the Daihai drainage basin indicating silicate limitation of primary productivity by diatoms phytoplankton in the Daihai Lake.