As concerns grow over the detrimental impacts of microplastics (MPs) on aquatic ecosystems, understanding their dynamics in Japanese biota has become increasingly urgent. We identified and compared MPs (diameter 20–5000 µm) in 11 organisms (fish, invertebrates, and a macroalga) and in sediments in the Tsurumi River estuary, Japan. A total of 1260 MPs were detected across all samples. The most common polymer was polyethylene (n = 492), followed by polypropylene (136) and polyamide (120). The mass concentration of MPs entangled in macroalgae was approximately two orders of magnitude higher than in sediment by wet weight. While there seemed to be no indication of increased bioaccumulation of MPs via trophic transfer, the results suggest that MP accumulation in macroalgae might play an important role in adverse effects of MPs on tidal flat organisms. Due to additional technical challenges, we were unable to process many samples. Further work is needed to clarify the dynamics of MPs in this area.