Reverse electrodialysis (RED) generates electricity from a mixture of seawater and river water. Herein, patterned membranes consisting of ultra-thin pore-filling membranes (16-μm thick) were used to determine whether the RED system operates steadily when using natural underground seawater and sewage effluent and if the membranes become polluted by various foulants. The flat stack performances, comprising flat membranes and woven-type spacers, were compared with those of the pattern stack, comprising patterned membranes with mirror-imaged wavy lines. The pattern stack clearly reduced the pressure drop and maintained the power within 40% of the initial value, and the flat stack significantly increased to 3 bar inside the sewage effluent and decreased the power to 20% of the initial value. Both anion and cation exchange-surface membranes showed organic fouling and scaling, with more significant fouling in the flat stack. The patterned membranes used here provide a powerful solution to reduce fouling inside RED stacks.