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We derive a radiative transfer equation that accounts for coupling from surface waves to body waves and the other way around. The model is the acoustic wave equation in a two-dimensional waveguide with reflecting boundary. The waveguide has a thin, weakly randomly heterogeneous layer near the top surface, and a thick homogeneous layer beneath it. There are two types of modes that propagate along the axis of the waveguide: those that are almost trapped in the thin layer, and thus model surface waves, and those that penetrate deep in the waveguide, and thus model body waves. The remaining modes are evanescent waves. We introduce a mathematical theory of mode coupling induced by scattering in the thin layer, and derive a radiative transfer equation which quantifies the mean mode power exchange.We study the solution of this equation in the asymptotic limit of infinite width of the waveguide. The main result is a quantification of the rate of convergence of the mean mode powers toward equipartition.