Multi-criteria decision-making in selection of wastewater treatment alternatives has been explored widely, while few past studies comprehensively addressed the integration of various aspects (e.g., environmental, economical, ecological and management, and technical factors), which is a priority for decision-makers. This paper develops the integrated fuzzy analytical hierarchy process (AHP) with multidimensional scaling (MDS) approach to improve current methods for determining the optimal alternative. The integrated method incorporates the weights computed by AHP into the fuzzy matter-element, and allows evaluators to understand the relative importance of each index or criterion at a high level. This is followed by the MDS method to determine the optimal alternative directly through the coordinates associated with each alternative in a two-dimensional configuration. The method was evaluated via specific programming language software packages, and was applied to select natural wastewater treatment alternatives in a case study. Results indicate the stabilization pond was the optimal alternative among five natural wastewater treatment systems. Sensitivity analysis was conducted and reflects the importance of weighing on alternative selection.