Despite increased awareness of threats against Critical Infrastructure (CI), securing of Supervisory Control and Data Acquisition (SCADA) systems remains incomplete. The majority of research focuses on preventative measures such as improving communication protocols and implementing security policies. New attempts are being made to use commercial Intrusion Detection System (IDS) software to protect SCADA systems. These have limited effectiveness because the ability to detect specific threats requires the context of the SCADA system. SCADA context is defined as any information that can be used to characterise the current status and function of the SCADA system. In this thesis the standard IDS model will be used with the varying SCADA data sources to provide SCADA context to a signature and anomaly detection engine. A novel addition to enhance the IDS model will be to use the SCADA data sources to simulate the remote SCADA site. The data resulting from the simulation is used by the IDS to make behavioural comparison between the real and simulated SCADA site. To evaluate the enhanced IDS model the specific context of a water and wastewater system is used to develop a prototype. Using this context it was found that the inflow between sites has similar diurnal characteristic to network traffic. This introduced the idea of using inflow data to detect abnormal behaviour for a remote wastewater site. Several experiments are proposed to validate the prototype using data from a real SCADA site. Initial results show good promise for detecting abnormal behaviour and specific threats against water and wastewater SCADA systems.