Natural systems offer an economic solution for the treatment of wastewater from small settlements. This study presents a detailed technical analysis of three stabilization pond systems designed to treat municipal wastewater, varying in capacity from 250 to 1400 population equivalent. Construction costs for the three systems were estimated using standard costing tables for public works for year 2010. The data from the three systems were used to derive empirical equations predicting the required facility surface area and construction cost as function of the design population. For the environmental impact assessment, two construction scenarios were examined: using reinforced concrete and using earthen structures. For the latter case, two options were tested: use of a synthetic geomembrane and use of a compacted clay layer as waterproofing materials. The environmental footprint was calculated for these scenarios applying the Life Cycle Analysis (LCA) methodology. It was concluded that soil structures, and particularly use of clay, had an overall economic and environmental advantage compared to reinforced concrete.