The effective dynamics of interacting waves for coupled Schrödinger-Korteweg-de Vriesequations over a slowly varying random bottom is rigorously studied. One motivation forstudying such a system is better understanding the unidirectional motion of interactingsurface and internal waves for a fluid system that is formed of two immiscible layers. Itwas shown recently by Craig-Guyenne-Sulem [1] thatin the regime where the internal wave has a large amplitude and a long wavelength, thedynamics of the surface of the fluid is described by the Schrödinger equation, while thatof the internal wave is described by the Korteweg-de Vries equation. The purpose of thisletter is to show that in the presence of a slowly varying random bottom, the coupledwaves evolve adiabatically over a long time scale. The analysis covers the cases when thesurface wave is a stable bound state or a long-lived metastable state.