Redox flow batteries (RFBs) are considered as a promising technology for reliable and durable grid-scale electricity storage. Ion-exchange membrane (IEM), as a critical component of RFBs, largely dictates the performance, durability and cost of RFB systems. Membrane fouling has frequently been observed in aqueous RFBs when IEM are employed with different redox electrolytes. However, very few studies have been conducted on its origin and the profound impact to the device performance. Based on several representative redox molecules and IEMs that are commonly used in aqueous pH neutral RFBs, we investigate the effect and mechanism of membrane fouling. Extensive electrochemical and spectroscopic characterizations reveal that the fouling of IEMs generally involves redox species possessing the same charge as the counterions of membrane and having a large partition coefficient, which accumulate inside the membrane and at the membrane/electrolyte interface, blocking the ion-exchange sites in the membrane and creating an electric field at the interface inhibiting ion transport. These findings provide useful guidance to membrane selection and optimization. • The formidable influence of membrane fouling on redox flow batteries is revealed. • An equivalent circuit is proposed to delineate the mechanism of membrane fouling. • Several representative membranes and redox species are extensively characterized. • Membrane deterioration results from both inside the membrane and the interface.