Understanding the relationship between environmental factors and public health is critical to improving sustainability at a sub-national level. Proposals to evaluate the status of environmental health in a region must consider factors including the diversity of indicators, geographical scale, incomplete or inaccurate data and the need for focused methodologies that capture the complexity of this subject. This paper presents the design of a system based on expert knowledge to assess environmental sanitation in cities in the Algarve region of Portugal. It was used fuzzy logic to assess uncertainties in the system. Conceptually, the use of fuzzy sets theory is simple and can integrate human expertise. The current proposal demonstrates the usefulness of aggregating information and opinion-based classifications to categorize municipalities according to their environmental health characteristics. The analysis shows that improved environmental sanitation conditions have been observed in municipalities located in the region's center. In the west, municipalities have worse conditions not only in environmental health but also in other sustainability indicators. A main feature of the system, presented here, is the ability for users to select variables to be considered by experts and opinion-makers without re-modeling, which allows the system to be adapted to different situations and scenarios. Therefore, the assessment method based on fuzzy logic is useful to investigators looking for a more systemic assessment of sustainability.