The recently published Daughter Directive on priority substances is the culmination of several years of effort by the European Commission to develop consistent, Europe-wide environmental quality standards (EQS) that are scientifically based and protective of Europe's surface waters. This commentary describes progress to date in deriving EQS under the Water Framework Directive and identifies some remaining challenges and opportunities. In the Daughter Directive, annual average EQS are set for surface waters for all 33 priority substances. No sediment standards are included, and biota EQS are proposed for methyl-mercury, hexachlorobenzene and hexachlorobutadiene. Important remaining questions include whether the standard chemical risk assessment methodology is appropriate for deriving water column EQS and whether it would be appropriate to derive EQS for sediment or biota or to adopt alternative strategies. Moreover, some cross-cutting issues about the cessation of discharges of naturally occurring or ubiquitous substances and the advantages and disadvantages of member states setting their own EQS are briefly addressed.