The fouling characteristics of dissolved organic matter (DOM) in the fresh water and seawater compartments of the reverse electrodialysis (RED) system were investigated under natural water conditions. The salinity gradient power generation was governed monovalent ions whereas multivalent ions strongly contributed to the fouling formation of the ion-exchange membranes (IEMs). The partial deposition of DOM within the membrane pores during its passage from the fresh water compartment to the seawater compartment facilitated the fouling formation of the IEMs. Despite of the similar DOC losses in fresh water (DOC loss = 20%) and seawater (DOC loss = 22%) through the RED system, the colour variations of the anion-exchange membranes (AEMs) and spacers in contact with fresh water were more noticeable than those in contact with seawater. These results indicate that the deposition of hydrophobic DOM components onto the AEM surfaces water may lead to the increases in the pressure drop of the fresh water compartment and the decreases in the power density of the RED system. Therefore, an appropriate pre-treatment strategy capable of mitigating membrane fouling by hydrophobic DOM components seemed to be indispensable to maintain constantly the performance of the RED system under natural water conditions.