In the context of rapid urbanization across Sub-Saharan Africa there is a critical need for more robust decision-making between different ways of providing sanitation services in existing and new peri-urban areas. In several countries, authorities tried to find solutions by developing strategies to address sanitation problems in the form of Strategic Sanitation Plans. In Burkina, Strategic Sanitation Plans have been elaborated and implemented since the 1990s. Fada N'Gourma, a secondary city in Burkina, also adopted a Strategic Plan for wastewater and excreta management in 2006. In this study we use material flow analysis as a decision making tool to verify technology options of the Plan. A model was developed and data was collected in order to assess material and nitrogen flows. The status quo situation was compared to scenario based on the proposals made in the Sanitation Plan. Results show that the technology options which were recommended improved human health in the short term. However, the options led to groundwater pollution in the medium term. Compared to the current situation, matter and nitrogen flows would increase by 7% and 7.4% respectively in groundwater. It is thus concluded that the proposed options will not achieve the Plan's stated objectives of environmental protection.