Coral atoll lagoons are typically connected to the bounding ocean by both deep channels and shallow reef flats. Reef flats are ubiquitous on atoll rims, interspersed between atoll islands, and flows here are primarily unidirectional; setup from wave breaking on reef flats create a lagoon-ward water level gradient that drives a flow into the lagoon. While this flow has a clear tidal variability, the magnitude is determined by the incoming wave energy and modified by the tide through depth-limited wave breaking. Results from a four-month deployment in Huvadhoo atoll in the Maldives, Indian Ocean, explore the relation between reef flat velocities and external forcing from offshore swell waves and tidal depth. Results show that tidal phase is an additional, important parameter, creating a lag between lagoon and ocean tides that opposes wave-generated setup on rising tides, and amplifies it on falling tides.