The poor access to data on the marine environment is a handicap to government decision-making, a barrier to scientific understanding and an obstacle to economic growth. In this light, the European Commission initiated the European Marine Observation and Data Network (EMODnet) in 2009 to assemble and disseminate hitherto dispersed marine data. In the ten years since then, EMODnet has become a key producer of publicly available, harmonised datasets covering broad areas. This paper describes the methodologies applied in EMODnet Geology project to produce fully populated GIS layers of seabed substrate distribution for the European marine areas. We describe steps involved in translating national seabed substrate data, conforming to various standards, into a uniform EMODnet substrate classification scheme (i.e., the Folk sediment classification). Rock and boulders form an additional substrate class. Seabed substrate data products at scales of 1:250,000 and 1:1 million, compiled using descriptions and analyses of seabed samples as well as interpreted acoustic images, cover about 20% and 65% of the European maritime areas, respectively. A simple confidence assessment, based on sample and acoustic coverage, is helpful in identifying data gaps. The harmonised seabed substrate maps are particularly useful in supraregional, transnational and pan-European marine spatial planning.