The European Water Framework Directive (WFD) was enacted in the year 2000 with a stepwise approach. After legal implementation in the various member states large efforts were undertaken for the initial characterization of water bodies, risk assessment, to implement extensive monitoring schemes and to develop management plans at different aggregation levels by the year 2010. The initial characterization process and risk assessment had to be finalized by 2004 and delineated water bodies including a typological classification and identified the significant pressures and impacts in a screening procedure. In parallel, monitoring programmes and new biological indicator systems were developed in order to proof and refine the results of the risk assessment with an ecological indicator based assessment in a subsequent step which was finalized in 2009. Although the risk assessment for Germany was based on existing data that were originally collected for other purposes and came from a large variety of environmental or economical sectors, the results differ only slightly from the monitoring and indicator based information with respect to classifications of the ‘ecological status’ and ‘chemical status’. From this result we conclude that a risk assessment based on a careful application and intelligent combination of existing data sources with proven quality allows the recognition of trends and the identification of priorities for action of measures already at an early stage of a management process. However, monitoring schemes and advanced sets of ecological indicators are essential in later management steps both for narrowing uncertainties remaining from the risk assessment and to allow for effect controls of implemented measures. Moreover, these monitoring indicators should differentiate the effects of multiple stressors more factor specific and with respect to ecosystem states and functions. In conclusion, we see risk and indicator based assessments as complementary elements in Integrated Water Resources Management (IWRM), which have to be linked in systematic and phased procedures.