In this study, an analytical procedure for simultaneous analysis of major anions Cl-, NO3-, SO4-, NO2- and H2PO4- in surface water and groundwater samples using portable capillary electrophoresis instrument has been developed and evaluated. The solution of histidine 12 mM adjusted to pH 4 with was selected as the background electrolyte buffer. A wide linear range with the linear correlation coefficient for the target anions (R2) more than 0.995 was obtained. The RSDs for peak areas and migration times were less than 10.1 percent and less than 2.1 percent respectively. Twenty surface water samples collected from different lakes in Hanoi city were analyzed with the developed method and a comparison was made with ion chromatography where the bias is or