In recent years, the implementation of digital twin (DT) as a digital replica of the physical asset has matured significantly in smart manufacturing with the advancement of digital technologies. At the same time, for water treatment facilities which are critical infrastructures, DT is still in its infancy for real-world applications. Therefore, there is a pressing need for research that can accelerate the DT development for these critical infrastructures.The aim of this study is to improve the performance of DT for water treatment facilities using probabilistic assessment. The scope of research focuses on two main directions: first, utilizing probabilistic machine learning (ML) models to assist in real-time anomaly detection of DT, and second, developing data assimilation methods for probabilistic ML models to obtain optimized system states for process control. Anomaly detection is crucial for water treatment facilities as they can be susceptible to cyber-physical attacks that negatively impact the system's functionality, while data assimilation can improve the robustness of real-time monitoring in noisy environments by assimilating ML predictions with observations. A combined anomaly detection framework (CADF) was first developed for DT applications using probabilistic ML models. A prototype water treatment testbed facility was utilized to verify the anomaly detection framework by simulating various types of security attacks. CADF utilizes a