A detailed understanding of microplastics (MPs) behaviour in freshwater ecosystems is crucial for a proper ecological assessment. This includes the identification of significant transport pathways and net accumulation zones, considering their inherent, and already proven influence on aquatic ecosystems. Bioavailability of toxic agents is significantly influenced by macroinvertebrates' behaviour, such as bioturbation and burrowing, and their prior exposure history. This study investigates the effect of bioturbation activity of Chironomus riparius Meigen, 1804 on the vertical transfer of polyethylene MPs ex-situ. The experimental setup exposes larvae to a scenario of 10× the environmentally relevant high concentration of MPs (80 g m−2). Bioturbation activity was estimated using sediment profile imaging with luminophore tracers. This study demonstrated that spherical MPs are vertically transferred in the sediment due to the bioturbation activity of C. riparius larvae and that their presence influences the intensity of the bioturbation activity over time. The present findings provide a noteworthy contribution to the understanding of the relationship between ecosystem engineers and the dispersion and accumulation of MPs within freshwater ecosystems.