Water is the main stimulus for the development of microorganisms, and its flow has an important role in the spreading of contaminants. In hospitals, the water distribution system requires special attention since it can be a source of pathogens, including those in the form of biofilms often correlated with resistance of microorganisms to various treatments. In this paper, information relevant to cases of nosocomial infections involving water circuits as a source of contaminants is compiled, with emphasis on the importance of microbiological control strategies to prevent the installation, spreading and growth of microorganisms in hospitals. An overview of the worldwide situation is provided, with emphasis on Brazilian hospitals. Different approaches normally used to control the occurrence of nosocomial infections due to waterborne contaminants are analyzed, and the use of the polysaccharide chitosan for this specific application is briefly discussed.