Interactions between microplastic (MP) and fine-grained suspended sediment in natural waters are important for the environmental fate of plastic particles. Estuaries are transitional areas between freshwater and open marine systems and are recognized as important accumulation zones for MPs. However, there is a knowledge gap on the processes driving the sedimentation of MPs in estuaries, especially with regard to positively buoyant MPs. Here we show from settling tube experiments that positively buoyant and non-spherical MP HDPE particles in different size-fractions (63–500 μm) and concentrations (1 and 5 mg l⁻¹) rapidly flocculate and settle with natural fine-grained sediment in natural seawater. Our results demonstrate that flocculation is a key process for the vertical transport of MP in estuaries. The implication is that land-based sources of positively buoyant HDPE MP transported by rivers will likely settle and accumulate in estuarine environments and thereby increase the concentration of MP in the benthic zone.