This chapter presents an approach to modeling smart city subsystems based on the principle of their cyber-physical integration into a single infrastructure. The uniqueness of the approach is the provision of the smart city topology as a set of cyber-physical clusters that ensure the functioning of the city. Unlike existing solutions, the proposed approach allows to consider the relationship of the information flows between different levels of smart city systems. Considered features of modeling of the cyber-physical water supply system (including active control system models, resource allocation models, scenario modeling) were put into practice by the smart city infrastructure in Saint Petersburg, Russia. The analysis of the functioning of the megalopolis water supply enterprise revealed significant vulnerabilities in ensuring the strategic security of the Leningrad Region, Russia. A basic list of recommendations for reducing the probability of water shortage has been developed based on scenario modeling of disabling of the main water supply source. These results are the basis for creating simulation models of interrupting the main source of smart city water supply and considering issues of improving the efficiency of water supply cyber-physical systems control in the smart city.