The effect of using methanol in the flush-solvent bottle of the auto-sampler of Ion Chromatograph on the determination of sulfate ions was studied using AS11-HC 2 mm analytical column. The use of 50% methanol in the flush solvent bottle results in overestimation of sulfate concentration by 18%. However, the use of 10% methanol instead of 50% did not show such error in the determination of sulfate using the same column. Furthermore, the effect of using OnGuard-RP and OnGuard-P cartridges for sample pretreatment on the determination of different anions was also studies using AS14-HC 2 mm analytical column. The results indicate that using OnGuard-RP cartridge caused the concentration of fluoride, bromide, nitrate, phosphate and sulfate ions to be underestimated, whereas the concentration of chloride ions to be overestimated. The error in the determination of fluoride, bromide, nitrate, phosphate sulfate, and chloride was found to be 40.0%, 26.0%, 22.8%, 26.8%, 18.0%, and 25.0% of the certified standard concentration, respectively. It was also found that the use of OnGuard-P cartridge resulted in underestimation of fluoride, chloride, bromide, nitrate, phosphate, and sulfate by 60.0%, 40.0%, 82.0%, 87.2%, 45.2%, and 39.0% of the certified standard concentration, respectively. These findings point out to careful corrections that should be considered in any application of ion chromatography utilizing such sample pretreatment.