We investigate the all-penetrating drift velocities, due to surface wave motion in an effectively inviscid fluid that overlies a saturated porous bed of finite depth. Previous work in this area either neglects the large-scale flow between layers [Phillips (1991)] or only considers the drift above the porous layer [(Monismith (2007)]. We propose a model where flow is described by a velocity potential above the porous layer, and by Darcy's law in the porous bed, with derived matching conditions at the interface between the two layers. The damping effect of the porous bed requires a complex wavenumber k and both a vertical and horizontal Stokes drift of the fluid, unlike the solely horizontal drift first derived by Stokes Stokes (1847) in a pure fluid layer. Our work provides a physical model for coral reefs in shallow seas, where fluid drift both above and within the reef is vitally important for maintaining a healthy reef ecosystem [Koehl et al. (1997), Monismith (2007)]. We compare our model with measurements by Koehl & Hadfield (2004) and also explain the vertical drift effects described in Koehl et al. (2007), who measured the exchange between a coral reef layer and the (relatively shallow) sea above.