Pulsed electric discharge has been used for the removal of iron colloid substances from aqueous solutions. The residual concentration of organic substances in aqueous solution depends on the pulse repetition rate. The maximum decrease in organic substances concentration was observed at the pulse repetition rate of 800 pps. Comparison of the results obtained for iron colloid solutions containing humic substances and solutions of humic subtances with no colloids shows that the highest removal efficiency of organic substances was obtained when no iron and silicon ions were present in the solution. The results of our experiments suggest that pulsed electric discharge treatment for the removal of organic substances from natural waters is more efficient at an aftertreatment stage, after precipitation of colloid substances.