The high accumulation potential of estuaries for plastics, particularly microplastics, poses a threat to the high societal value and biodiversity they provide. To support a spatially refined evaluation of the risk that microplastic pollution poses to fauna utilizing estuarine sedimentary habitats, we investigated the distribution of microplastics (lower limit of quantification, LOQ = 62 μm) at the sediment surface of two dominant habitats, and subsequently compared microplastic burdens between two crabs species utilizing these habitats. Microplastics were dominated by low density polyolefins (45–50 %), comparable to the polymer composition of macroplastics. The vast majority (99 %) of microplastics were ≤1 mm, and increased exponentially (with an exponent of 2.7) in abundance at smaller sizes, hinting at three-dimensional fragmentation. Our results suggest that the presence of vegetation needs to be accounted for in risk assessments with small microplastics (≥62 μm and ≤1 mm) on average 2.6 times more prevalent within reed beds compared to mudflats. Additionally, sediment properties also play a role with an exponential decrease in small microplastic abundance at coarser sediments, increased organic matter content, and decreased water content. These results suggest that at specific locations, such as the study area, local sources can provide a substantial contribution to microplastic contamination. To translate these habitat- and site-specific differences into a risk assessment relevant for macroinvertebrates, ecological traits such as differences in feeding modes should be accounted for, as we found substantial differences in both size and abundance of microplastics in gastrointestinal tracts of two crab species, Chiromantes dehaani and Chasmagnathus convexus, with different feeding modes. Display omitted •We aimed to support a spatially refined risk evaluation of microplastics in estuaries.•Microplastics were about 2.6 times more prevalent within reed beds than mudflats.•Microplastic abundance decreased exponentially with larger sediment grain size.•A power-law decrease in microplastic size hinted at three-dimensional fragmentation.•Microplastic size and abundance differed between crabs with different feeding modes.