The research of trace element behaviour and size fractionation is significant to understand the processes in the water-rock system. Moreover, the aqueous speciation of trace elements is strongly related to their distribution and toxicity. In this research, trace elements behaviour and their size fractionation are investigated in the natural water (the surface water and shallow groundwater) of the Ganjiang River and Xiushui River basins. Trace element concentrations were measured by ICP-MS. The authors estimated the size fractionation of the trace elements between suspended forms (>0.45m) and dissolved fractions, which included truly dissolved (1 kDa) and colloidal particles (0.45m-1 kDa)), after filtration through a 0.45 m acetate cellulose membrane filter. The distinct features of the trace element size fractionation were identified. The size fractionation of the trace elements under different conditions (in the surface water and shallow groundwater) was studied.