The exchange of mass and momentum between surface and subsurface flows across bed surfaces plays a crucial role in sediment dynamics, particularly for incipient sediment motion. While experimental studies have elucidated these interaction mechanisms, recent advancements in computational fluid dynamics (CFD) have enabled detailed investigations into incipient sediment motions. Interface-resolved simulations, which achieve high fluid resolution around sediment particles, have successfully linked incipient motion to small-scale fluid phenomena. However, conventional resolved simulations of sediment transport have primarily focused on unidirectional flow, with limited studies under wave fields due to the complexities of modeling water surface deformations. This study simulates the incipient motion of spherical sediment under shallow waves using a coupled Discrete Element Method (DEM) and an enhanced Moving Particle Semi-implicit (MPS) method. An interface-resolved model is developed using the Immersed Boundary Method (IBM). Simulations are conducted on both impermeable and permeable beds to comparatively investigate the effect of interstitial flow. Our results indicate that rapid penetration flow into permeable beds generates high dynamic pressure on the lower stoss side of the spherical particles, significantly influencing their incipient motion.