Emerging global threats, such as climate change, urbanization and water depletion, are driving forces for finding a feasible substitute for low cost-effective conventional activated sludge (AS) technology. On the other hand, given their low cost and easy operation, nature-based systems such as constructed wetlands (CWs) and waste stabilization ponds (WSPs) appear to be viable options. To examine these systems, a 210-day experiment with 31 days of peak load scenario was performed. Particularly, we conducted a deliberate strategy of experimentation, which includes applying a preliminary study, preliminary models, hypothetical tests and power analysis to compare their removal efficiencies and resilience capacities. In contrast to comparable high removal efficiencies of organic matter-around 90%-both natural systems showed moderate nutrient removal efficiencies, which inferred the necessity for further treatment to ensure their compliance with environmental standards. During the peak period, the pond treatment systems appeared to be the most robust as they indicated a higher strength to withstanding the organic matter and nitrogen shock load and were able to recover within a short period. However, high demand of land-2.5 times larger than that of AS-is a major concern of the applicability of WSPs despite their lower operation and maintenance (O&M) costs. It is also worth noting that initial efforts on systematic experimentation appeared to have an essential impact on ensuring statistically and practically meaningful results in this comparison study.