Reverse electrodialysis (RED) is a process to harvest renewable energy from salinity gradients. Under lab conditions with artificial salt solutions, promising results have been achieved in recent years. However, in large scale industrial applications, natural waters are used and that poses challenges such as fouling. Fouling of anion exchange membranes (AEMs) by organic matter (e.g. humic acids) has been identified as a possible cause that lowers RED performance with natural waters. In this work, natural river and seawater at the Afsluitdijk (The Netherlands) are used to study the RED performance of six different AEMs. These AEMs are characterized before and after RED experiments with natural waters. The effect of natural fouling is found to be specific for each AEM and highly dependent on their respective chemistries and associated membrane properties. Firstly, aromatic AEMs with a low swelling degree showed a permselectivity decrease as well as membrane resistance increase. Secondly, aliphatic AEMs with a medium swelling degree experienced only a membrane resistance increase. Finally, only a decrease in permselectivity was observed for aliphatic AEMs with large swelling degrees. Subsequently, the effect of AEM fouling is compared to the observed decrease in RED performance and this shows that AEM fouling can only explain a minor part of the losses in open circuit voltage (OCV). The RED power densities dropped by 15–20% over 12 days, independent of the AEMs selected, while the reduced AEM performance could only explain 2–4% of this reduction in power density. This demonstrates that next to AEM fouling, also other factors, such as spacer fouling, are expected to be the dominant fouling mechanism, reducing the performance to a much larger extent.