Natural disasters can damage or destroy critical infrastructures, which underpin the delivery of essential services such as power, water, health, communications and banking. Disruption to critical infrastructure can cause catastrophic losses and adverse economic impacts. In the past few years climate change has increased the number and severity of natural disasters. Consequently, the importance of protecting critical infrastructure has greatly increased in national security and risk management strategies around the world. Many countries have developed a range of strategies for strengthening the resiliency of their infrastructure. These strategies, however, similar to any other decision-making strategies, are subject to uncertainty and a comprehensive critical infrastructure protection strategy is required to be able to reduce exposure to risk and address uncertainty. This chapter reviews the possible uncertainties associated in protection strategies and introduces some approaches to deal with these uncertainties. The chapter then focuses on the use of Bayesian networks as a framework for resilience planning of critical infrastructure through framing adaptive capacity of Emergency Management and its relationship to enhancing resilience and decreasing vulnerability.