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The chemistry of major cations (Mg~(2+), Ca~(2+), Na~+, and K~+) and anions (HCO_3~-, SO_4~(2-),and Cl~-) in the water of Lake Pumayum Co and its inflow river was studied, revealing the obvious ionic difference among various inflow rivers and the lake. The chemical type of the lake water was Mg~(2+)Ca~(2+)-HCO_3~--SO_4~(2+), but the major ions of the main inflow rivers were Ca~(2+)-Mg~(2+)-HCO_3~-. In the lake inlet of Jiaqu River, the main inflow river, there was significant variance of water chemistry within the depth less than 2 m. However, it was almost homogeneous at other area of the lake. Therefore, with the evidence of distribution of water chemistry and oxygen isotope of lake water, a conclusion can be outlined that Jiaqu River had a distinct effect on the hydrochemistry of the water on the submerged delta, whereas this is not the case for other rivers. The Gibbs plot revealed that the dominant mechanism responsible for controlling chemical compositions of the lake water was rocks weathering in the drainage area. Ion ratios and ternary plots further explored the main processes controlling the water chemistry of the catchment, i.e., carbonate weathering, pyrite weathering, and silicate weathering. The different hydrochemistry characteristics between river water and lake water may result from the CaCO_3precipitation. The findings will benefit the explanation of the environmental significance of carbonate in paleolimnological studies in the lake.