Endocrine-disrupting chemicals (EDCs) are a reason for growing concern because of their substantial and long-lasting deleterious effects on human health and wildlife populations. These include direct effects on aquatic organisms and may be a concern to species feeding on the aquatic food chains and water, including humans. In the European Community, the dedicated legislative tools to protect the aquatic environment and human health from contaminants released to surface waters is the Water Framework Directive (WFD). The achievement of protection goals is assessed through the comparison of concentrations measured in the media and thresholds of no effect called Environmental Quality Standards (EQSs). As EDCs are explicitly mentioned in the WFD, an analysis of the state of the art was undertaken on how far and how consistently ED properties were considered in the derivation of EQS values. Our results reveal substantial heterogeneity according to substance and that among substances with ED evidences, EQSs have been derived without considering ED properties for 70% of them. A methodology to better consider endocrine disrupting properties is proposed and includes a logical and systematic approach to derive EQSs with a proposal to specify additional assessment factors based on the specific hazard and potential uncertainty.