We have designed and characterized a simple Rayleigh-surface acoustic wave-based micropump, integrated directly with a fully enclosed 3D microfluidic system, which improves significantly the pumping efficiency within a coupled fluid whilst maintaining planar integration of the micropump and microfluidics. We achieve this by exploiting the Rayleigh-scattering angle of surface acoustic waves into pressure waves on contact with overlaid fluids, by designing a microfluidic channel aligned almost co-linearly with the launched pressure waves and by minimizing energy losses by reflections from, or absorption within, the channel walls. This allows the microfluidic system to remain fully enclosed—a pre-requisite for point-of-care applications—removing sources of possible contamination, whilst achieving pump efficiencies up to several orders of magnitude higher than previously reported, at low operating powers of 0.5 W