The European Union sets Environmental Quality Standards (EQS) for 33 + 8 “priority or priority hazardous substances”; Hg being included in the latter group. Directive 2008/105/EC fixes EQS for total Hg concentration in filtered water (0.45 µm) and allows Member States to opt for an alternative EQS for biota. However, proposal COM 2011/876, currently under discussion, sets to reverse this approach by requiring the application of a biota-based EQS of 20 ng g−1 total Hg wet weight and specifying, at the time of writing, that this EQS is intended for fish. The biota EQS is meant for the protection of piscivorous wildlife against secondary poisoning and should protect the aquatic ecosystems and human health. Adopting a biota-based EQS for Hg reflects current scientific understanding, with most Hg-related environmental issues arising from the biomagnification of methylmercury (meHg) rather than direct Hg (or meHg) toxicity via water exposure. An EQS for biota also automatically accounts for Hg bioavailability issues, thus greatly increasing the possibility to identify situations requiring risk management during routine monitoring programs. Depew et al. (2012) derived a threshold concentration of 40 ng g−1 wet weight for reproductive effects in fish following dietary exposure to meHg. Besides protecting piscivorous organisms, the proposed EQS is therefore amenable to application for the protection of prey fish. However, adoption of the EQS for biota is likely to pose enormous pressure on regulatory agencies. Looking at fish collected from some European lakes and rivers during 2005–2010, Hg concentrations exceed the proposed EQS by 2- to 16-fold (Table 1). Table 1, albeit far from exhaustive, includes representative water bodies and should reflect the range of Hg contamination in fish from European surface waters. How to reconcile the scientific superiority of the EQS for biota with regulatory compliance, therefore, represents a major conundrum. Guilizzoni (2011) Pessina (2010) Pola (2011) Pola (2011) Ortelli et al. (2009) Babut et al. (2011) ICPR (2011) In this respect, proposal COM 2011/876 makes specific provision for substances behaving as ubiquitous persistent bioaccumulative and toxic (UPBT) substances. If there is a robust statistical monitoring baseline, Member States can justify failure in meeting the EQS for an UPBT by presenting separate classification maps showing that the “bad” status is caused by an UPBT for which all possible measures have been taken. The same proposal allows Member States to apply an EQS for different matrices, provided they demonstrate that it achieves the same level of protection as the EQS for biota. Other arguments, not stated in the proposal, include the application of the EQS for biota to invertebrate groups (expected to have lower Hg concentrations) or, in a purely pragmatic way, a revision of the numerical EQS value to make it less stringent. Reverting to a water-based EQS is not advisable because of the scientific superiority of the standard for biota and, similarly, revision of the EQS numerical value is difficult to justify on a scientific basis. As to the other possibilities, application of the EQS to invertebrates will protect forage fish against dietary Hg exposure (Depew et al. 2012), but EQS for piscivorous wildlife and forage fish may not be interchangeable. Finally, the choice of including Hg in the list of UPBT would shift focus from the national to the global scale, thus reducing efforts to target important local issues. For example, lakes Maggiore and Lugano have contiguous catchments, but current Hg concentrations in fish (Table 1) reflect the long history of Hg contamination of Lake Maggiore through the 20th century and require specific basin-scale measures for remediation. Overall, the impact of Hg on European waters may be much more serious than previously thought. The practical problems of such situations are obvious, but most recent scientific evidence confirms rather than questions the solidity of the proposed numerical value. Regulatory agencies must therefore expand Hg monitoring of biota to fully appreciate the gap between the targeted and the current situation. With more information, specific cases possibly allowing for the use of less stringent EQS for the same level of protection may be identified. Further research on global and local Hg biogeochemical cycles along with ecologically meaningful investigation of Hg ecotoxicology, rather than shortcuts to reduce noncompliance, therefore appear as the correct way to reinforce the successful marriage of science and policy exemplified by the Hg EQS for biota.