Water CIs are exposed to a wide number of IT challenges that go from the cooperation and alignment between physical and cyber security teams to the proliferation of new vulnerabilities and complex cyber-attacks with potential disastrous consequences. Although novel and powerful solutions are proposed in the literature, most of them lack appropriate mechanisms to detect cyber and physical attacks in real time. We propose a Cross-Layer Analytic Platform (denoted as CLAP) developed for the correlation of Cyber and Physical security events affecting water CIs. CLAP aims to improve the detection of complex attack scenarios in real time based on the correlation of cyber and physical security events. The platform assigns appropriate severity values to each correlated alarm that will guide security analysts in the decision-making process of prioritizing mitigation actions. A series of passive and active attack scenarios against the target infrastructure are presented at the end of the paper to show the mechanisms used for the detection and correlation of cyber–physical security events. Results show promising benefits in the improvement of response accuracy, false rates reduction and real-time detection of complex attacks based on cross-correlation rules.