Worldwide, water security is adversely affected by factors such as population growth, rural–urban migration, climate, hydrological conditions, over-abstraction of groundwater, and increased per-capita water use. Water security modeling is one of the key strategies to better manage water safety and develop appropriate policies to improve security. In view of the growing global demand for safe water, intelligent methods and algorithms must be developed. Therefore, this paper proposes an integrated interval type-2 Fuzzy VIseKriterijumska Optimizcija I Kompromisno Resenje (IT2FVIKOR) with unsupervised machine learning (ML). This includes IT2FVIKOR for ranking and selecting a set of alternatives. Unsupervised machine learning includes hierarchical clustering, self-organizing map, and autoencoder for clustering, silhouette analysis and elbow method to find the most optimal cluster count, and finally Adjusted Rank Index (ARI) to find the best comparison within two clusters. This proposed integrated method can be divided into a two-phase fuzzy-machine learning-based framework to select the best water security strategies and categorize the polluted area using the water datasets from the Terengganu River, one of Malaysia’s rivers. Phase 1 focuses on the IT2FVIKOR method to select five different strategies with five different criteria using five decision makers for finding the best water security strategies. Phase 2 continues the unsupervised machine learning where three different clustering algorithms, namely, hierarchical clustering, self-organizing map, and autoencoder, are used to cluster the polluted area in the Terengganu River. Silhouette analysis is applied along with the clustering algorithms to estimate the number of optimal clusters in a dataset. Then, the ARI is applied to find the best comparison within the original data with hierarchical clustering, self-organizing map, and autoencoder. Next, the elbow method is applied to double-confirm the best clusters for each clustering algorithm. Last, lists of polluted areas in each cluster are retrieved. Finally, this 2-phase fuzzy-Machine learning–based framework offers an alternative intelligent model to solve the water security problems and find the most polluted area.