Terrorism is a crucial danger to the world, especially the Middle East. As Jordan is amidst countries with armed conflicts, its natural resources (in particularly, water resources) are vulnerable to terrorist attacks. In this paper, possible biological and chemical weapons that can be used as intimidation, along with their threats, vulnerabilities, and inactivation methods, concerning water treatment processes in the municipality of Irbid, are studied. Irbid is the second largest city in terms of population in Jordan, after the capital city of Amman, and it is the nearest governorate to Syria borders that is considered a war zone. After conducting risk assessment that takes into consideration criticality, threats, and vulnerability, it appears that only one of the eight units, which is the Makhraba pumping station, along with the Bushra water tank, were identified as medium risk. The other units have treatment processes and proper precautions that are able to inactivate or prevent any possible contamination. A response plan should be set by developing a telemetry system with specific sensors that can detect any sudden and unacceptable threats to the water quality and that has the ability to shut down the concerned units automatically.