Oil sands process-affected water (OSPW), a by-product of bitumen extraction through surface mining in Alberta, Canada, contains various constituents of concern, including naphthenic acid fraction compounds (NAFCs). These organic compounds are particularly worrisome due to their toxicity and persistence in the environment. Constructed wetland treatment systems (CWTS) use plants and their associated microbes to attenuate contaminants in wastewater. Field-scale CWTS have been presented as a potential large-scale treatment option for OSPW, specifically for degrading NAFCs. To optimize the use of CWTS for large-scale treatment of NAFCs in OSPW, it is essential to deepen our understanding of various design parameters and explore ways to enhance efficacy. Mesocosm-scale experiments serve as a valuable intermediary, bridging the gap between complex field trials and controlled laboratory settings. Mesocosms provide a controlled, replicable environment to study the effects of various parameters such as substrate, plant species, temperature, and retention time while incorporating ecological complexities in their design. Published and previous work has shown that this method is successful in evaluating the impacts of different parameters on the efficacy of CWTS to attenuate NAFCs in OSPW. This protocol outlines the design and setup of a surface flow wetland mesocosm, along with the experimental approach for treating NAFCs in OSPW. This method can be adapted to treat other wastewaters across diverse geographical locations.