Particles containing alpha (α) nuclides were identified from sediment in stagnant water in the Unit 3 reactor building of the Fukushima Daiichi Nuclear Power Station (FDiNPS). We analyzed different concentrations of α-nuclide samples collected at two sampling sites, the torus room and the main steam isolation valve (MSIV) room. The solids in the stagnant water samples were classified, and the uranium (U) and total alpha concentrations of each fraction were measured by dissolution followed by inductively coupled plasma mass spectrometry and α-spectrometry. Most of the α-nuclides in the stagnant water samples from the torus and MSIV rooms were in particle fractions larger than 10 μm. We detected uranium-bearing particles ranging from sub-µm to 10 µm in size by scanning electron microscopy–energy-dispersive X-ray (SEM–EDX) observations. The chemical forms of U particles were determined in U–Zr oxides, oxidized UO2, and U3O8 with micro-Raman spectroscopy. Other short-lived α-nuclides (plutonium [Pu], americium [Am], and curium [Cm]) were detected by alpha track detection, and the particles with α-nuclides was characterized by SEM–EDX analysis. α-nuclide-containing particles with several tens to several 100 µm in size mainly comprised iron (Fe) oxyhydroxides. In addition, we detected adsorbed U onto Fe oxyhydroxide particles in the MSIV room sample, which indicated nuclear fuel dissolution and secondary U accumulation. This study clarifies the major characteristics of U and other α-nuclides in sediment in stagnant water in the FDiNPS Unit 3 reactor building, which significantly contribute to the consideration of removal methods for particles containing α-nuclides in the stagnant water.