The WFD is an overarching piece of legislation that aims to harmonize existing European water policy; since 2000 it requires managing the river basins so that the quality and quantity of water does not affect the ecological services and to promote sustainable water use of any specific water body. Nevertheless the goals of other directives, such as drinking water, bathing water and urban wastewater treatment (UWWT), are not yet harmonised mainly concerning microbiological and PS/PSR/PHS contamination. Great challenges are due to emerging contaminants especially the technical improvement and harmonisation for risk identification and risk assessment: for biological effects and for chemical analysis and, finally integrate this knowledge to preserve the “good status”. The methodologies implemented have as aim the identification of acceptable or unacceptable risks. This identification provides the basis for the regulatory decisions, which follow from the risk assessment. After priority setting the UWWT needs to be adjusted and existing or new treatment options should comply with the requirements of the different directives. This will be another step on the way to reach the targets given in EU water legislation and in the achievements of millennium development goals.