We tested the hypothesis that mineralization of molybdenum unreactive phosphorus (MUP) in pore water is the major pathway for the changes in the concentration of molybdenum-reactive P (MRP) in pore water and inorganic P in sediment particles. The concentration of inorganic P in the sediment particles increased from December to April in Lake Kasumigaura, whereas concentrations of organic P in the sediment particles and MUP in pore water decreased. These results suggest that MUP mineralization plays a key role as the source of MRP, whereas desorption of inorganic P from the sediment particles into the pore water is a minor process. One-dimensional numerical simulation of sediment particles and the pore water supported the hypothesis. Diffusive flux of MUP was small in pore water, even in near-surface layers, so mineralization was the dominant process for changing the MUP concentration in the pore water. For MRP, diffusion was the dominant process in the surface layer, whereas adsorption onto the sediment was the dominant process in deeper layers. Researchers usually ignore organic P in the sediment, but organic P in sediment particles and the pore water is a key source of inorganic P in the sediment particles and pore water; our results suggest that in Lake Kasumigaura, organic P in the sediment is an important source, even at depths more than 1 cm below the sediment surface. In contrast, the large molecular size of MUP in pore water hampers diffusion of MUP from the sediment into the overlying water.