Understanding the effects of fishing fleets on both target and non-target species and managing these effects are essential to achieve Good Environmental Status (GES) for marine ecosystems. The use of high resolution fishing effort data in environmental studies has allowed significant scientific progress with respect to the environmental impacts of real fishing fleets and provided a more realistic perspective on the wider ecological consequences of fishing disturbance. A new EU council regulation and its interpretation, aimed at protecting the confidentiality rights of individual fishers, are currently hampering scientific access to this high-resolution effort data and thus are endangering the provision of management advice based on best available knowledge. This study argues that the withholding of this information will seriously undermine the quality and accuracy of scientific output and ultimately damage fishers' livelihoods through poorly advised management. Furthermore, the council regulation runs contrary to the EU's initiative for greater transparency and its commitment to implement an ecosystem approach to fisheries management and the preservation of ecosystem services. The interpretation of the new EU council regulation by local administrations can thus only be viewed as a significant step back from these aims. Ultimately, while trying to protect fishers' rights it may work to their disadvantage and that of society.