Abstract: Sample pretreatment methods in the determination of Fe, Mn, Zn, Pb, Cu, Ni, Cr and Cd in surface water and underground water samples by GFAAS, ICP-AES and ICP-MS were studied. Two sample pretreatment methods of 0.45 μm filtering and acid digestion were compared. The results showed that the analytical results from filter pretreatment method were lower than those from acid digestion method. The cause for the problem is considered due to that some microbes in water adsorbing some trace elements and lost in the filtering process, which causes the lower analytical results for some elements. Therefore, the suggestion was proposed that water samples should be treated by acid digestion at low temperature before the instrument determination.