This paper focuses on the investigation and systematization of cyber threats to largescale cyber-physical systems with dynamic network infrastructures. The proposed taxonomy provides a unified view of the specifics of such systems in terms of security, attacker targets, and TCP/IP network stack levels. Taken together, the systematization developed provides the basis for a new technology to protect complex dynamic systems by providing knowledge of which networking parameters need to be controlled to counteract certain classes of cyberthreats.