The seepage and transport of pore water and fine particles on the seabed have an important impact on the dynamic process of seabed deposition and the stability of seabed. To solve the difficulty in describing the seepage development process and quantifying the seepage mass of fine particles on seabed, we used white magnesium hydroxide powder that has good physical and chemical stability at seabed to indicate and qualify the process of fine sediments seepage via stratified sampling, reacting with hydrochloric acid, and ion chromatography. Experiments and analysis indicate that the proposed method could clearly describe the whole seepage development process including the upward migration of fine particles, the formation of different-scaled seepage channels, and the reach of partial tracer to the seabed surface, from which the seabed silt movement under cyclic load-induced excess pore water pressure and upward seepage pressure gradient were clearly presented and thus quantitative characterization of the layer-by-layer seepage of fine particles from the interior of the seabed to the bed surface was realized. This study in silt seabed. Moreover, the proposed method achieves quantitative characterization of the seepage mass of fine particles from the interior to the surface of seabed, which provides a practical tool for further clarify the coupling mechanism and developing quantitative evaluation methods of wave-induced liquefaction, seepage, and re-suspension of silt seabed.