Industrial Control Systems (ICS) such as water and power are critical to any society. Process anomaly detection mechanisms have been proposed to protect such systems to minimize the risk of damage or loss of resources. In this paper, a graphical model-based approach is proposed for profiling normal operational behavior of an operational ICS referred to as SWaT (Secure Water Treatment). Timed automata are learned as a model of regular behaviors shown in sensors signal like fluctuations of water level in tanks. Bayesian networks are learned to discover dependencies between sensors and actuators. The models are used as a one-class classifier for process anomaly detection, recognizing irregular behavioral patterns and dependencies. The detection results can be interpreted and the abnormal sensors or actuators localized due to the interpretability of the graphical models. This approach is applied to a dataset collected from SWaT. Experimental results demonstrate the model's superior performance on both precision and run-time over methods including support vector machine and deep neural networks. The underlying idea is generic and applicable to other industrial control systems such as power and transportation.