Wastewater is a valuable resource that requires effective treatment management solutions on a global scale. Wastewater has become a major source of irrigation in peri-urban areas in developing countries. Natural treatment systems (NTS) have recently gained appeal in peri-urban environments due to their lower cost and maintenance requirements. The operating efficiency of natural systems was tested in this study using case studies from Vizianagaram, Andhra Pradesh, India. The efficacy of nutrient (Phosphorous and Nitrogen content) and organic matter removal was investigated in four NTS with varying operation maintenance and loading rates. According to the study, Natural treatment systems have a lot of potential for treating peri-urban wastewater. Waste-stabilization systems outperform systems based on duckweed and hyacinth plants, according to the findings. Regularly maintained and operated systems have an organic and nutrient removal efficiency of over 80%, outperforming others. According to the findings, decentralized, well-maintained Waste Stabilization Ponds (WSP) provide a feasible, self-sustaining, and environmentally beneficial wastewater treatment option for rural irrigation water.