Microplastic particles can be deposited to sediments and subsequently ingested by benthic organisms. It is unknown to what extent ingestion of microplastic is taxon-specific or whether taxa can be selective toward certain types of microplastics. Here, we used state-of-the-art automated micro-Fourier-transform infrared (μFTIR) imaging and attenuated total reflectance FTIR spectroscopy to determine small-size (20–500 μm) and large-size (500–5000 μm) microplastic particles in sediments and a range of benthic invertebrate species sampled simultaneously from the Dommel River in the Netherlands. Microplastic number concentrations differed across taxa at the same locations, demonstrating taxon-specific uptake, whereas size distributions were the same across sediments and taxa. At the site with the highest concentration, microplastic occupied up to 4.0% of the gut volume of Asellidae. Particle shape distributions were often not statistically different between sediments and taxa, except for Astacidea at one of the locations where the proportion of particles with a length to width ratio >3 (i.e., fibers) was twice as high in sediments than in Astacidea. Acrylates/polyurethane/varnish was predominately found in sediments, while soft and rubbery polymers ethylene propylene diene monomer and polyethylene-chlorinated were the dominant polymers found in invertebrates. Microplastic polymer composition and thus polymer density differed significantly between invertebrates and their host sediment. Trophic transfer at the base of the food web appears to have a filter function with respect to microplastic particle types and shapes. Together with the very high ingestion rates, this has clear implications for ecological and human health risks, where uptake concerns edible species (e.g., Astacidea).