There is a growing demand for integrating an assessment tool to select wastewater treatment alternatives based on sustainability in the Jordanian wastewater sector. The sector in Jordan has a unique and critical situation that has raised concerns among stakeholders, including donors, and international and national organizations, to carefully select a sustainable treatment system for each case. The Jordanian government set a tool to distinguish between treatment systems, and this tool is mainly focused on financial criteria. However, the sector needs to integrate assessment tools with a wider consideration of other sustainability criteria. Usually, stakeholders are not equipped with a clear methodology to perform sustainability assessments. Therefore, this study proposes and develops a Multi-Criteria Analysis (MCA) tool to evaluate wastewater treatment alternatives from a sustainability perspective for a case study in Jordan—Al Azraq town. Firstly, the study explored the decision and organizational context of the wastewater sector through several interviews. Secondly, assessment criteria and indicators were proposed to compare three proposed treatment alternatives. Finally, the Analytical Hierarchy Process (AHP) was applied with composite scores to evaluate wastewater treatment alternatives. Finally, The results of the composite scores indicated that French Constructed Wetland (FCW) was the best option for this case study, with a score of 3.13, followed by Stabilization Pond (SP) as the second sustainable option, with a score of 2.67, and lastly, Activated Sludge (AS), with a score of 2.07. Several conclusions have been highlighted during the process development, such as the importance of selecting sustainability indicators carefully, and engaging stakeholders during the design and implementation of the assessment.