Over two billion (109) people have no or limited access to sanitation and more than two-thirds of these unserved people are also found in the rural communities. As still many areas in the Philippines use septic tank systems, most effluent is likely to be discharged without proper treatment and contributes to “nutrient pollution” to water bodies. Those poorly designed or maintained septic tanks may also result in an increased incidence of waterborne diseases in rural areas. Eco-toilet system (ETS) offers an innovative solution for nutrient recovery on a household or community level. Large-scale implementation of eco-toilet systems can contribute towards water footprint reduction and increased availability of nutrients for the cultivation of food crops. Such implementation is challenging as this requires high social acceptance due to the transition from a water-dependent facility to waterless technology. To address this challenge, key social, behavioral, and political barriers are needed to be identified. Influential barriers are needed to be determined and prioritized to increase implementation scale; however, uncertainties are present, and evaluating these barriers will be a problem. In this study, a neutrosophic Decision-Making Trial and Evaluation Laboratory (DEMATEL) approach is used to identify and analyze the barriers to implementing ETS. Neutrosophic sets have been used to represent uncertainties by accounting for incomplete, vague, inconsistent, inaccurate, and subjective data or expert judgment. The uncertainty is addressed by treating responses in terms of their membership, non-membership, and indeterminacy towards the intended meaning of the response. A case study is presented to illustrate the approach.