Healthcare facilities require flexible layouts that can adapt quickly in the face of various disruptions. COVID-19 confirmed this need for both healthcare and manufacturing systems. Starting with the transfer of decision support systems from manufacturing, this paper generalizes layout re-design activities for complex systems by presenting a simulation framework. Through a real case study concerning the proliferation of nosocomial cross-infection in an intensive care unit (ICU), the model developed in systems dynamics, based on a zero order immediate logic, allows reproducing the evolution of the different agencies (e.g., physicians, nurses, ancillary workers, patients), as well as of the cyber-technical side of the ICU, in its general but also local aspects. The entire global workflow is theoretically founded on lean principles, with the goal of balancing the need for minimal patient throughput time and maximum efficiency by optimizing the resources used during the process. The proposed framework might be transferred to other wards with minimal adjustments; hence, it has the potential to represent the initial step for a modular depiction of an entire healthcare facility.