Sequential permeability and chemical osmosis experiments on Wakkanai mudstones were performed to explore the relationships between the semipermeability of clayey rocks and the hydraulic and diffusion parameters as well as the pore structure characteristics. The wide ranges in osmotic efficiency (0.0004–0.046) and intrinsic permeability (8.92 × 10−20 to 1.24 × 10−17 m2) reflect the variation in the pore size distributions of the Wakkanai mudstones. A regression analysis between osmotic efficiency and permeability shows that the osmotic efficiency is proportional to the inverse of permeability, suggesting that the permeability is indeed indicative of the degree of semipermeability. Osmotic efficiency was determined invariant with the effective diffusion coefficient for the Wakkanai mudstones (3.59–8.36 × 10−11 m2/s) due to their small osmotic efficiencies (≤0.046). The wide variation in osmotic efficiencies and pore structure characteristics of Wakkanai mudstones indicates that the nanoscale pores enable semipermeability in Wakkanai mudstones. However, the pressure evolution caused by chemical osmosis is limited by the connected wide pores that are the main conduits for water, thus dissipating the osmotic pressure buildup induced by the semipermeability of nanoscale pores.