The European Union (EU) aims at increasing the share of renewable energy use, of which nearly half originates from wood sources currently. An energy supply from wood sources strongly relies on green water resources, which are limited and also essential for food security and terrestrial biodiversity. We have estimated the water footprint (WF) of wood for energy consumed in the EU-28 (WFwec) by combining data on energy produced from wood sources in the EU per member state for the year 2015 from the EU energy reference scenario 2016, extra-EU trade in fuelwood and charcoal, and country-specific estimates of the water footprint per unit of wood. We find that the WFwec is large (156 × 109 m3/y), 94% of this footprint is situated within the EU, and it is almost exclusively related to green water (99%). Adding WFwec to the WF related to the EU’s consumption of agricultural and industrial products as well as domestic water use (702 × 109 m3/y) signifies an increase of 22% to 858 × 109 m3/y. We show that over half of the internal WFwec is in member states that have a high degree of green water scarcity and hence very limited potential left to sustainably allocate more green water flows to biomass production. The results of this study feed into the debate on how the EU can achieve a sustainable and reliable energy supply. Policies on energy security should consider that increased use of wood or other biomass for energy increases the already significant pressure on limited green water resources.