European Union Directive 2013/39/EU, which amended and updated theWater Framework Directive (WFD; 2000/60/EC) and its daughter directive (2008/105/EC), sets Environmental Quality Standards for biota (EQSbiota) for a number of bioaccumulative chemicals. These chemicals pose a threat toboth aquatic wildlife andhumanhealth via the consumptionof contaminated prey or the intake of contaminated food originating from the aquatic environment. EU member states will need to establish programs to monitor the concentration of 11 priority substances in biota and assess compliance against these new standards for the classification of surface water bodies. An EU-wide guidance effectively addresses the implementation of EQSbiota. Flexibility is allowed in the choice of target species used for monitoring to account for both diversity of habitats and aquatic community composition across Europe. According to that guidance, the consistency and comparability of monitoring data across member states should be enhanced by adjusting the data on biota contaminant concentrations to a standard trophic level by use of the appropriate trophic magnification factor (TMF), ametric of contaminant biomagnification through the food web. In this context, the selection of a TMF value for a given substance is a critical issue, because this field-derivedmeasure of trophicmagnification can show variability related to the characteristics of ecosystems, the biology and ecology of organisms, the experimental design, and the statistical methods used for TMF calculation. This paper provides general practical advice and guidance for the selection or determination of TMFs for reliable application within the context of the WFD (i.e., adjustment of monitoring data and EQS derivation). Based on a series of quality attributes for TMFs, a decision tree is presented to help endusers select a reasonable and relevantTMF.