Our paper presents a model of economic impacts arising from disruptions to critical infrastructures. This model is a component of the Critical Infrastructure Protection Decision Support System (CIP/DSS) which simulates the dynamics of a set of interconnected individual infrastructures. We use factors of production (such as energy, telecommunications, and labor) from the CIP/DSS model to estimate the effects of interruptions to these infrastructures. The system dynamics approach we use is compared to equilibrium-based approaches such as input-output modeling. This method allows an understanding of the economic benefits of various protective measures. We incorporate non-equilibrium dynamics that arise from these disruptions to provide values for various economic impacts such as lost revenues and lost sales. The results from a disruption due to an infectious disease outbreak are presented. We show that the effects of quarantine dominate the overall economic impacts in a number of cases.