Modern shipping ports require computer systems to accommodate an increasing number of port calls, larger vessel sizes, and tighter supply chains. Disruptions to assets on these networks have the potential to propagate to other critical infrastructures at great economic cost. Such disruptions may be introduced intentionally by adversaries that include nation states, organized crime, hacktivists, and insiders. Area Maritime Security Committees (AMSCs) must develop security plans to minimize disruptions' impact. This paper explores one way to couple a simulation of the flow of commodities through a shipping port with an optimization that minimizes the cost of disruptions to the port transportation system. Our intent is to enable stakeholders to run what-if scenarios, to understand the impact and effect of cyber-physical disruptions, and to optimally mitigate their effect. This research, based on ongoing fieldwork with Port Everglades and the USCG, hopes to improve security policies that integrate cyber and physical effects.