Cyber physical systems are critical to the infrastructure of a country. They are becoming more vulnerable to cyber attacks due to their use of off the shelf servers and industrial network protocols. Availability on World Wide Web for monitoring and reporting, has further aggravated their risk of being attacked. Once an attacker breaches the network security, he can affect the operations of the system which may even lead to a catastrophe. Mathematical and formal models try to detect the departure of the system from its expected behaviour but are difficult to build, and are sensitive to noise. Furthermore they take a lot of time to detect the attack. We here propose a behaviour based machine learning intrusion detection approach that quickly detects attacks at the physical process layer. We validate our result on a complete replicate of the physical and control components of a real modern water treatment facility. Our approach is fast, scalable, robust to noise, and exhibits a low false positive (FP) rate with high precision and recall. The model can be easily updated to match the changing behaviour of the system and environment.