Experimental results from various pilot-scale configurations of natural treatment systems as means for wastewater treatment are demonstrated. Various systems consisting of waste stabilization ponds, shallow algal ponds and water hyacinth ponds were operated in parallel, series or mixed arrangement in order to find the optimum setting that enables efficient effluent quality to be reused for agricultural purposes. The results indicate that waste stabilization ponds were very efficient for wastewater treatment, especially in terms of organic and nutrient load removal, achieving an effluent quality able to be used for restricted irrigation. However, coliform numbers were not always consistent with the proposed guidelines. To cope with the problem, a modified configuration employing water hyacinth ponds, waste stabilization ponds and final water hyacinth ponds is proposed. The results indicate that the latter system provides a considerable degree of treatment compared to previous systems, yielding an effluent able to be used for irrigated agriculture and related applications.