Critical infrastructure systems (CIS) are complex large-scale systems which in turn require highly sophisticated supervisory control systems to ensure that high performance can be achieved and maintained under adverse conditions. The global CIS Real-Time Control (RTC) need of operating in adverse conditions involves, with a high probability, sensor and actuator malfunctions (faults). This problem calls for the use of an on-line Fault Detection and Isolation (FDI) system able to detect such faults. This paper proposes a FDI mechanism that extends the classical Boolean fault signature matrix concept taking into account several fault signal properties to isolate faults in CIS. To exemplify the proposed FDI scheme in CIS, the Barcelona drinking water network is used as a case study.