A critical review of the last 25 years of dioxin policy in the Elbe river catchment is presented along seven main theses of the River Basin Community (RBC)-Elbe background document “Pollutants” for the Management Plan 2016–2021. In this period, polychlorinated dibenzodioxins/-furans (PCDD/Fs) and dioxin-like polychlorinated biphenyls (dl-PCBs) will play a major role: (i) as new priority substances for which environmental quality standards (EQSs) need to be derived (Directive 2013/39/EC); (ii) in the search for innovative solutions in sediment remediation (i.e., respecting the influence of mechanical processes; Flood Risk Directive 2007/60/EC); and (iii) as indicators at the land–sea interface (Marine Strategy Framework Directive 2008/56/EC). In the Elbe river catchment, aspects of policy and science are closely connected, which became particularly obvious in a classic example of dioxin hot spot contamination, the case of the Spittelwasser creek. Here, the “source-first principle” of the first cycle of the European Water Framework Directive (WFD) had to be confirmed in a controversy on the dioxin hot spots with Saxony-Anhalt’s Agency for Contaminated Sites (LAF). At the Spittelwasser site, the move from “inside the creek” to “along the river banks” goes parallel to a general paradigm shift in retrospective risk assessment frameworks and remediation techniques for organic chemicals (Ortega-Calvo et al. 2015). With respect to dioxin, large-scale stabilization applying activated carbon additions is particularly promising. Another important aspect is the assessment of the ecotoxicology of dioxins and dl- PCBs in context of sediment mobility and flood risk assessment, which has been studied in the project framework FloodSearch. Currently, the quality goals of the WFD to reach a “good chemical status” are not met in many catchment areas because substances such as mercury do and others probably will (PCDD/Fs and dl-PCB) exceed biota-EQS values catchment area-wide. So far, relating biota-EQS values to sediment-EQSs is not possible. To overcome these limitations, the DioRAMA project was initiated, which has led to improved approaches for the assessment of dioxin-contaminated sediment using in vitro bioassays and to a robust dataset on the interrelation between dioxins and dioxin-like compounds in sediments and biota.