A part of the radiocaesium from the Fukushima Daiichi Nuclear Power Plant (FDNPP) accident was emitted as glassy, water-resistant caesium-bearing microparticles (CsMPs). Here, we isolated and investigated seven CsMPs from marine particulate matter and sediment. From the elemental composition, the 134Cs/137Cs activity ratio, and the 137Cs activity per unit volume results, we inferred that the five CsMPs collected from particulate matter were emitted from Unit 2 of the FDNPP, whereas the two CsMPs collected from marine sediment were possibly emitted from Unit 3, as suggested by (i) the presence of calcium and absence of zinc and (ii) the direction of the atmospheric plume during the radionuclide emission event from Unit 3. The presence of CsMPs can cause overestimation of the solid–water distribution coefficient of Cs in marine sediments and particulate matter and a high apparent radiocaesium concentration factor for marine biota. CsMPs emitted from Unit 2, which were collected from the estuary of a river that flowed through a highly contaminated area, may have been deposited on land and then transported by the river. By contrast, CsMPs emitted from Unit 3 were possibly transported eastward by the wind and deposited directly onto the ocean surface.