Globally, the numerous efforts exerted toward providing basic sanitation services to people have not been sufficient to achieve universal coverage. In developing countries worldwide, many policies, strategies, initiatives, and projects on basic sanitation have failed, despite important investments. Of the several reasons explaining the failure, it is remarkable to note that such approaches have focused mainly on improving the technology of the sanitation system without considering the human aspects, such as user preferences. Moreover, there is currently no comprehensive approach that ensures the provision of a sanitation service that users want or need to satisfy their needs. In this regard, this study proposed an approach to identify the variables and indicators that represent user preferences in the selection and creation of more holistic sanitation strategies, technologies, systems, and services. The proposed approach was applied in rural communities of Chiapas, the poorest state of Mexico, and was effective in identifying user preferences, which suggests that it could be an intrinsic part of the design, planning, and implementation process toward leading rural communities to achieve sustainable development goals on universal basic sanitation. The evaluation results also demonstrated that among the preferences linked to the technical features, esthetics, costs of the system, and socioeconomic-related aspects were the most important to be considered in the provision of basic sanitation. The study points out the necessity of understanding how culture, preferences, practices, and socioeconomic conditions directly affect the possibilities for users to gain access to basic sustainable sanitation services.