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The Wadden Sea is the world’s largest intertidal area and a UNESCO World Heritage Site. Macrozoobenthic invertebrates perform key ecological functions within intertidal areas by regulating nutrient cycles, decomposing organic matter, and providing food for fish, birds and humans. To understand ecological processes and human impacts on biodiversity, the Synoptic Intertidal BEnthic Survey (SIBES) has sampled intertidal macrozoobenthos since 2008. On average 4,109 stations across 1,200 km² of Dutch Wadden Sea mudflats are sampled from June to October to quantify the benthic invertebrate community and sediment composition, including species abundance and biomass, and grain size and mud content. The dataset published now contains 51,851 sampled stations with 3,034,760 individuals of 177 species. This paper details data collection, validation and processing methods. SIBES is ongoing and data will be updated yearly. In sharing these data, we hope to enhance collaborations and understanding of the impact of various pressures on macrozoobenthic invertebrates, sediment composition, food webs, the ecosystem, and biodiversity in the Wadden Sea and other intertidal habitats.