Here, we present SIBES-data on median grain size (micrometer) and mud content (%) of sediment, and abundances (#) and biomass (g) of benthic invertebrate found at sampling stations on intertidal mudflats of the Dutch Wadden Sea. SIBES stands for Synoptic Intertidal BEnthic Survey and is a long-term ecological time-series performed by NIOZ. It is aimed at understanding ecological processes and sediment dynamics of intertidal mudflats related to benthic invertebrates. Details of the sampling method, laboratory protocols and data curation can be found in the accompanying paper in the journal "Scientific Data" (https://doi.org/10.1038/s41597-025-04540-9). In summary, roughly 4,500 stations are sampled yearly from 2008 and onwards. The most recent 3 years are under embargo, but available upon request to the corresponding author. Samples were collected on a 500 m grid and on randomly located stations in the months June to October. Stations were not sampled at the same dates across years. Sampling stations were visited by foot during low tide and by boat during high tide. At each site sampled by boat, two cores were taken to a depth of ~25 cm (combined area of 0.0173 m2). Samples were sieved on a 1 mm round mesh in the field. After sieving, large bivalves were separated from the other species and frozen at -20 degrees Celsius to allow for easier process in subsequent laboratory analysis. From the remaining sample, all benthic invertebrates were collected and preserved at a 4% formaldehyde solution. Sediment samples were taken with a small core with a diameter of 33 mm from the surface of the inter-tidal flats to a depth of 4 cm and then frozen at -20 degrees C. In the laboratory, organisms were identified and counted and their biomass determined as ash-free dry-mass (AFDM). Sediment samples were freeze-dried and grain size distributions measured with a particle size analyser. For further details concerning methods, processing, data curation, analyses and R-scripts, we refer to the accompanying paper. When using these data, please cite that paper (https://doi.org/10.1038/s41597-025-04540-9). An R-library with examples of analysing and plotting the data is provided online at https://github.com/allertbijleveld/sibes. 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. (2023-12-06)