Effects of the embedded monopile foundation on the local distributions of pore water pressure, soil stresses, and liquefaction are investigated in this study using a three-dimensional integrated numerical model. The model is based on a Reynolds-Averaged Navier-Stokes wave module and a fully dynamic poroelastic seabed module and has been validated with the analytical solution and experimental data. Results show that, compared to the situation without an embedded foundation, the embedded monopile foundation increases and decreases the maximum pore water pressure in the seabed around and below the foundation, respectively. The embedded monopile foundation also significantly modifies the distributions of the maximum effective soil stress around the foundation and causes a local concentration of soil stress below the two lower corners of foundation. A parametric study reveals that the effects of embedded monopile foundation on pore water pressure increase as the degrees of saturation and soil permeability decrease. The embedded monopile foundation tends to decrease the liquefaction depth around the structure, and this effect is relatively more obvious for greater degrees of saturation, greater soil permeabilities, and smaller wave heights.