Cybersecurity has become an emerging challenge for business information management and critical infrastructure protection in recent years. Artificial Intelligence (AI) has been widely used in different fields, but it is still relatively new in the area of Cyber-Physical Systems (CPS) security. In this paper, we provide an approach based on Machine Learning (ML) to intelligent threat recognition to enable run-time risk assessment for superior situation awareness in CPS security monitoring. With the aim of classifying malicious activity, several machine learning methods, such as k-nearest neighbours (kNN), Naïve Bayes (NB), Support Vector Machine (SVM), Decision Tree (DT) and Random Forest (RF), have been applied and compared using two different publicly available real-world testbeds. The results show that RF allowed for the best classification performance. When used in reference industrial applications, the approach allows security control room operators to get notified of threats only when classification confidence will be above a threshold, hence reducing the stress of security managers and effectively supporting their decisions.