For a two-dimensional problem and at microwave radar frequencies, this paper presents a method to compute the field scattered by a highly conducting (the impedance boundary condition is applied) rough sea surface in the presence of a duct having a linear-square refractive index profile below a medium of constant refractive index. In a previous paper, the corresponding Green's function, which allows us to solve the propagation problem, has been derived without considering the sea surface. Using the boundary integral equation (BIE) method, this paper solves jointly the scattering problem from the sea surface and the propagation problem by including this Green's function in the BIE. In addition, to efficiently solve the linear system obtained from the method of moments by discretizing the integral equations, the forward-backward method is applied, which allows us to consider very long rough surfaces.