The principal stresses that occur in soil below ground level often change direction due to engineering activities. A typical example would be the cyclic loading applied by waves and currents onto the foundation of offshore structures. Even though the principal stress rotations (PSR) are recognized as some kind of “loading” that is exerted onto seabed soil, it is ignored in most investigations into how soil around marine structures responds to ocean waves and currents. In response this paper will simulate the fluid-seabed-structure interactions (FSSI) while considering the impact of PSR. This simulation will utilize an integrated numerical model in which VARANS equations are used for the flow motion. A coupled fluid-dynamic framework and a generalized plasticity model will be developed for the saturated porous medium to examine the cyclic loading of seabed and the continuous rotation of principal stress orientations. It is predicted that the stress path in the τxz versus (σx′−σz′) plane around the structure will denote variations in deviator stress in conjunction with the rotations of the principal stress axis. The mechanical impact of PSR becomes most significant in the region beneath the breakwater and up to a depth of the half thickness of the seabed. Ignoring the PSR-induced deformation may lead to an underestimation of (p̄PSR−p̄no−PSR)∕γwd by 35% in this region. •An integrated model for the nonlinear interaction between wave–current, a submerged breakwater and its foundation soil is developed.•The cyclic behaviour of seabed soil is reproduced using a generalized plasticity approach concerning the impact of principal stress rotation.•The predicted stress path in the τxz versus σx′−σz′ plane denotes variations in the deviator stress and rotations of principal stress axes.•Ignoring the PSR-induced deformation may lead to an underestimation of (p̄PSR−p̄no−PSR)∕γwd by 35% in the region underneath the breakwater.