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Here we present the first digital, publicly available, ecotope map of the trilateral Wadden Sea covering the Netherlands, Germany and Denmark. This ecotope map, representative for the time period 2008–2012, was developed on the basis of bathymetry, salinity, flow velocity, exposure time, sediment composition, hard substrates and salt marshes. Ecotopes are discrete classes of the physical environment based on the distributions of communities in an ecosystem. An ecotope map can give a first–order estimate of the potential spatial distribution of species and communities. The use of a single, consistent and well-defined ecotope system made it possible to compare the proportions of the different ecotopes and compare properties of the tidal basins over the entire trilateral Wadden Sea. The 39 tidal basins within the Wadden Sea were clustered in four distinct types, using an unsupervised clustering algorithm. These four types included: 1) basins that are characterised by a large proportion of low-dynamic low-littoral ecotopes, 2) basins with a high proportion of high-dynamic sublittoral ecotopes, 3) shallow basins with over 50% low-dynamic mid-littoral ecotopes and 4) basins with an equal distribution of low-dynamic low-littoral and low-dynamic mid-littoral ecotopes. The clustering in four major tidal basin types gives clear guidance for comparative ecological and morphological studies between tidal basins. The ecotope map can be used for environmental research, policy and conservation purposes of the trilateral Wadden Sea in an integrated manner. • We produce the first digital, publicly available trilateral Wadden Sea ecotope map. • Tidal basins of the Wadden Sea were clustered in four main types. • The power law relation between channel and basin area was confirmed for all 39 basins. [ABSTRACT FROM AUTHOR]