Small on-site sanitation systems are widely present in suburban and rural areas in many countries. As these systems often underperform and have an impact on receiving waters, understanding their overall sustainability is of interest for policy and decision-makers. However, the definition and estimation of indicators defining sustainability are challenging, as it is finding the methodological approach to combine qualitative and quantitative indicators into one comprehensive assessment. In this study, twelve indicators defined by environmental, economic, social, technical and health-related criteria were used to compare nine alternatives of on-site sanitation for single households. A non-compensatory method for multi-criteria decision analysis, ELECTRE III, was used for the assessment together with weights assigned to each indicator by a reference group. Several scenarios were developed to reflect different goals and a sensitivity analysis was conducted. Overall, the graywater-blackwater separation system resulted as the most sustainable option and, in terms of polishing steps for phosphorus removal, chemical treatment was preferred over the phosphorus filter, both options being implemented together with sand filters. Assessing the robustness of the systems was a crucial step in the analysis given the high importance assigned to the aforementioned indicator by the stakeholders, thus the assessment method must be justified. The proposed multi-criteria approach contributes to aid the assessment of complex information needed in the selection of sustainable sanitation systems and in the provision of informed preferences. © 2019 The Royal Society of Chemistry.