Climate changes and urbanization push cities to redesign their drainage systems, which may increase separate stormwater discharges to local recipients. In the EU, regulation of these is governed by the Water Framework Directive (WFD) and the Floods Directive, but national implementation varies and is often supplemented with local non-legislative guidelines. By reviewing trends and discrepancies in the Danish regulation practice for separated stormwater discharges, this article investigates how the directives are put into effect. A legislative gap for separate stormwater discharges introduces uncertainty in the discharge permit conditions, which especially affect conditions targeting water quality. We point to several topics to be addressed, e.g., the level at which the regulation of separate stormwater discharges takes place, opportunities for coordination with flood risk and climate change adaptation initiatives, as well as uncertainties regarding the application of Best Available Techniques. Working with these issues would elevate the regulation practice and aid regulators in reaching a more holistic and consistent approach, thus improving chances of reaching the desired recipient status before or after the WFD deadline in 2027. This could be undertaken at river basin, river basin district or national level, but there is also potential for harvesting mutual benefits by addressing these challenges internationally.