Intertidal mudflat systems are shaped by geological processes and an interplay of hydrodynamics, sediment availability and ecological processes. All around the world these systems are affected by relative sea level rise (RSLR), changing climate and by human activities such as sediment nourishments, dredging, hydrological engineering and bottom trawling. These kinds of perturbations cause changes in morphology and sediment composition which may cause shifts in the composition, spatial distribution and productivity of benthic communities. We analysed the spatial and temporal variability of the sediment grain size of more than 900 km2 intertidal flats in the Dutch Wadden Sea in the period 2009–2019. The large scale coverage was achieved by yearly grid sampling at more than 4000 stations. Spatial panel data models were used to analyse changes in median grain size and mud content between years and to estimate the effects of resuspension due to wind and the accumulation of silt during summer. We show that between years the sediments of the intertidal flats changed synchronously throughout the study area and that the flats became coarser during the period 2011–2015 and muddier again between 2015 and 2019. The system wide changes and the absence of clear local deviations leads to the hypothesis that a large scale factor like changing hydrodynamic regime (e.g. due to RSLR), variability in the composition of suspended sediment in the North Sea or changing microphytobenthic productivity were causally involved in the coarsening of intertidal flats. Our data and analysis provides a base for further scientific enquiry but longer time series on higher temporal resolution of both sediment data and the physical and ecological environment are required. Models simulating the environment may provide further insight into possible development of sediment composition of the intertidal flats of the Wadden Sea.