Advances in mobile and pervasive computing, electronics technology, and the exponential growth in Internet of Things (IoT) applications and services has led to Building Automation System (BAS) that enhanced the buildings we live by delivering more energy-saving, intelligent, comfortable, and better utilization. Through the use of integrated protocols, a BAS can interconnects a wide range of building assets so that the control and management of asset operations and their services can be performed in one protocol. Moreover, through the use of distributed computing and IP based communication, a BAS can implement remote monitor and control in adaptive and real-time manner. However, the use of IoT and distributed computing techniques in BAS are leading to challenges to secure and protect information and services due to the significant increase in the attack surface and the inherent vulnerabilities of BAS integrated protocols. Since there is no intrusion detection and prevention available for BAS network, proposing a reliable security mechanism which can monitor the behavior of BAS assets becomes a major design issue. Anomaly Based Intrusion Detection is a security mechanism that uses baseline model to describe the normal behaviors of a system, so that malicious behaviors occurred in a system can be detected by comparing the observed behavior to the baseline model. With its ability of detecting novel and new attacks, Anomaly based Behavior Analysis (ABA) has been actively pursued by researchers for designing Intrusion Detection Systems. Since the information acquired from a BAS system can be from a variety of sources (e.g. sensors, network protocols, temporal and spatial information), the traditional ABA methodology which merely focuses on analyzing the behavior of communication protocols will not be effective in protecting BAS networks. In this dissertation we aim at developing a general methodology named Context Aware Anomaly based Behavior Analysis (CAABA) which combines Context Awareness technique with Anomaly based Behavior Analysis in order to detect any type of anomaly behaviors occurred in Building Automation Systems. Context Awareness is a technique which is widely used in pervasive computing and it aims at gathering information about a system's environment so it can accurately characterize the current operational context of the BAS network and its services. The CAABA methodology can be used to protect a variety of BAS networks in a sustainable and reliable way. To handle the heterogeneous BAS information, we developed a novel Context Aware Data Structure to represent the information acquired from the sensors and resources during execution of the BAS system which can explicitly describe the system's behavior. By performing Anomaly based Behavior Analysis over the set of context arrays using either data mining algorithm or statistical functions, the BAS baseline models are generated. To validate our methodology, we have applied it to two different building application scenarios: a smart building system which is usually implemented in industrial and commercial office buildings and a smart home system which is implemented in residential buildings, where we have achieved good detection results with low detection errors.