Abstract Background Due to the high number of immunosuppressed and other predisposed patients hospitals have to control and ensure the microbiological water quality. The origin for the occurrence of pathogenic microorganisms in water pipes is the formation of biofilm. Methods For the permanent control of water safety a water safety plan (WSP) was realized as recommended by the WHO following the principle "search and destroy". The WSP is based on an established HACCP concept due to the special focus. The most important measures include the concept for sample taking depending on patient risk. 3 different categories) are distinguished: risk area1 (high infection risk), risk 2 (moderate infection risk), and risk area 3 (not increased infection risk). Additionally to the threshold value of the German law for the quality of drinking water (TrinkwV) three more limiting values were defined (warning, alert, and worst case) for immediate risk adapted reaction. Additional attention has to be focussed on lavatory sinks, which are an open bacterial reservoir. Therefore continuous disinfecting siphons were installed as part of the WSP in high risk areas. If extended technical equipment is not available, especially for immunocompromised patients the following measures are easy to realize: boiled (or sun exposed) water for nursing procedures as well alimentary use, no showering. Results Comparing data over 3 years the microbial water quality was significantly improved resulting in no new case of nosocomial Legionella pneumoniae and decrease in neonatal sepsis. Conclusion According to average situations with highly contaminated water system the management must be defined with implementation of water task force, immediate providing of special equipment, information of patients and staff and control of the water quality, an example for successful decontamination of the hospital within 24 hours is given.