Abstract: A system and method for continuously monitoring the intake of a fresh water system to detect pathogens, chemicals, and other biological contaminants. The apparatus consists of a number of monitoring and containment facilities which are inserted into a fresh water intake pipe at various locations. The monitoring and containment facilities detect a hazard in the incoming water, send a signal to shut down the main intake pump, and collect samples of water immediately adjacent the monitoring and containment facility that detected the hazard. A signal may also be sent to a regulatory agency and to the Department of Homeland Security. The method consists of conducting a qualitative and quantitative analysis of water in a fresh water intake pipe; testing for hazards, and shutting down the main intake pump if a sufficient level of hazard is detected. The method also consists of collecting water samples for later analysis and of notifying the appropriate agencies.