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Most of development programs in sanitation encourage the building of infrastructure such as treatment plants that are unfortunately rapidly abandoned for reasons that are not well understood. A methodology to assess these factors for wastewater and faecal sludge treatment plants was developed, presenting the key factors and their type of influence on the system in three domains: institutional management, technical conception and financial and energetic resource balance. It offers a participatory tool for improving the planning and operation of treatment plants through an indicator list elaborated and tested during a case study in Senegal which is organized in six categories: (i) organizational basis at national level, (ii) sub-criteria acting as a springboard at all level, (iii) organizational basis at the office level, (iv) means and skills set-up, (v) planning and conception studies quality, and (vi) practical management of plant operation. Seven steps of analysis were developed to understand the point of view of local stakeholders, model the correlation between factors and define priorities to improve the system. Technical and operational difficulties are an important area of concern but they are not at the source of the problem. They are determined by decisions concerning the whole sanitation sector at a national level. Thus, the system can be improved only by considering the combination of several factors. The priority aspects are those which concern institutional management and financial strategies. The solution has to be adapted to the context and accepted by the local stakeholders.