While the European Union (EU) has one of the most extensive and sophisticated supranational water policy worldwide, its transboundary governance framework has certain structural deficiencies that may eventually give rise to significant cooperation gridlocks over shared river basins. Most prominently, EU water law as well as the numerous European basin treaties almost comprehensively ignore transboundary water quantity management and allocation questions. This lacuna is due to a series of hydro-geographical, political and institutional factors prevailing at the time when the foundations of today's European framework of transboundary water governance were laid down in the 1980s and 1990s. Yet, changing hydrological conditions points to increasing fluctuations in water quantities in European river basins. Due to their one-sided ecological focus, however, the existing European governance mechanisms may prove unable to handle a growing competition for water among riparian states in case of flow variations beyond historical ranges. This article investigates the roots and the possible future implications of the unresolved transboundary allocation question within the EU.