Here, recommendations to improve ecological and chemical status assessments in accordance with the European Water Framework Directive (WFD) are made on the basis of experience gained from the MODELKEY project database, linking existing biological and chemical monitoring data of 3 case study river basins (Elbe, Scheldt, and Llobregat). The data analysis within and across river basins revealed major obstacles to be tackled, including scarcity of matching ecological and chemical monitoring sites for cause–effect relationships as well as a general lack of stressor-specific metrics for single biological quality elements (BQE) to enable a comprehensive risk assessment of all predominant stressors, including toxicity. An example of such a metric, which is recommended for the BQE of benthic macroinvertebrates, is the trait-based species-at-risk index (SPEAR) that correlated well with a respective measure for toxic stress, referred to as toxic units, based on simple mixture toxicity concepts. Surprisingly, the assessment of chemical status of a total of 695 monitoring sites for 2000 to 2004 showed that environmental quality standards (EQSs) were exceeded for at least 1 of the currently 41 priority pollutants (PPs) in 92% to 98% of the cases in all 3 of the river basins, which, according to definition, indicates potential effects on ecological status. A comparison of compliance with EQSs for 41 PPs with a respective effect threshold (derived for benthic macroinvertebrates) revealed that the rather conservative concept of chemical status is most likely not protective in all cases. Furthermore, to account for the many other compounds that are detected frequently in European surface waters and that may also have ecotoxicological effects, we introduced a provisional predicted no-effect concentration that is in accordance with the EQS methodology and is suggested to identify potential emerging compounds for which no or insufficient toxicity data exist. In conclusion, this study aims to support the implementation of the WFD by drawing conclusions from the analysis of heterogeneous data sets of various member states and by introducing new tools to move toward an integrated European assessment of ecological and chemical status.