In this study, a methodology for disabling a multi-sensor cyber-physical system (CPS) is considered. By disabling the cyber-physical system is meant to simulate deliberate interference in the functioning of the system, checking the Lyapunov stability and determining a set of measures to improve the functioning. The M2 methodology is based on the system deactivation and determination of cyber-physical water supply systems (CPWSS) stability. The purpose of the methodology is to generate a list of requirements for the CPS. These requirements are the feedback loop of the cyber-physical system model. It is possible to improve the security level of the CPS operation of smart cities. In the example of the created methodology of CPS deactivation it was possible to evaluate CPWSS to carry out simulation of deactivation and to form the list of requirements to water supply systems for modern smart cities. Research is based on the methodologies of security and functioning of modern CPS and knowledge of the problems of water resources control.