Flows on coral reefs are forced by waves, tides, and winds (Monismith, 2007). The effect of waves on the mean flow momentum balance was described by Longuet-Higgins and Stewart (1964), who introduced the concept of a radiation stress gradient. Energy is dissipated as waves break on sloping beaches and reefs, and the resulting onshore radiation stress gradient is balanced by an offshore pressure gradient, creating wave setup. On a reef flat with a deeper lagoon behind it, wave setup drives a flow across the reef and into the lagoon (Gourlay, 1996a;Symonds et al., 1995). The mechanism of wave setup on submerged reefs can lead to remarkable dynamics, for example, Callaghan et al. ( 2006) who described two South Pacific atolls where the water level always exceeded the ocean water level due to wave pumping.While wave-driven flow is ubiquitous on shallow reefs with persistent waves, it is clear that not all reefs respond to wave forcing in the same way. To first order, the dynamical response depends on geometry