EU legislation, laid down in the Water Framework Directive, demands to minimize emissions of nitrogen, phosphate and crop protection products to achieve an excellent chemical and ecological quality in 2015. The aim is to force growers to a better water and disease management. Supply water of excellent chemical quality will have to be recirculated as long as possible, for which adequate disinfection equipment have to be used. Several sources of water are used as supply water. Rainwater is chemically best, followed by reverse osmosis water. However, the latter is rather expensive. Tap water and surface water often have a too high salinity, while well water may vary dramatically from place to place. Rainwater and surface water are potential risk factors for importing soil-borne pathogens. Disinfection of the recirculating nutrient solution can be done adequately by heat treatment and UV radiation. Membrane filtration performs well, but is mostly too costly. Chemical treatments as sodium hypochlorite, chlorine dioxide and copper silver ionization may partly solve the pathogen problem, but introduce a potential accumulation of other elements in closed systems. Hydrogen peroxide, chlorine dioxide and sodium hypochlorite perform better to clean pipe work instead of soil-borne pathogens.