In the context of sediment characterization, layer interface roughnesses may be responsible for sound-speed profile measurement uncertainties. To study the roughness influence, a three-dimensional (3D) modeling of a layered seafloor with rough interfaces is necessary. Although roughness scattering has an abundant literature, 3D modeling of spherical wave reflection on rough interfaces is generally limited to a single interface (using Kirchhoff-Helmholtz integral) or computationally expensive techniques (finite difference or finite element method). In this work, it is demonstrated that the wave reflection over a layered medium with irregular interfaces can be modeled as a sum of integrals over each interface. The main approximations of the method are the tangent-plane approximation, the Born approximation (multiple reflection between interfaces are neglected) and flat-interface approximation for the transmitted waves into the sediment. The integration over layer interfaces results in a method with reasonable computation cost.