Physical oceanographic observations were made with subsurface, taut-line moorings at Egmont Island, a tropical atoll within the Chagos Archipelago in the central Indian Ocean, to elucidate the dynamics of near-bed cold-water intrusions implicated in driving local aggregations of reef manta rays (Mobula alfredi). Manta have been previously shown to aggregate within ‘Manta Alley’, a lipped gully at 65 m depth along the north coast, at times when the surface to bottom temperature difference was highest. We here identify the dynamical processes driving these temperature differences and shaping the foraging landscape at Egmont, and equivalent small-scale atolls, improving our understanding of manta behavior at hotspots where they are most vulnerable to exploitation.The thermal regime within Manta Alley is shown to be governed at several spatiotemporal scales. The extreme 2019 Indian Ocean Dipole event drove a depression of the 26 °C isotherm to a depth of 115 m precluding the observation of cooling within the alley. As the thermocline shoaled with the change in phase of the IOD, near bed cold water flushing was seen with tidal periodicity within the gully. The internal tide is accompanied by high frequency internal waves with periods of O (5 min) which are shown to promote mixing through shear instability, evidenced by subcritical Richardson numbers, with surface-seabed temperature differences ∼4 °C observed throughout a tidal period.Our results highlight a level of heterogeneity in oceanographic dynamics at sub-atoll spatial scales within an environment in which these processes are rarely resolved. Whilst the physical mechanisms through which these dynamics drive foraging within the resident manta population remain unclear, the generation of turbulence by high frequency internal wave events as shown here may influence zooplankton distributions, improving feeding efficiency at discrete locations within atolls. Our results thus highlight the need to account for fine scale changes in oceanographic conditions when attempting to explain habitat utilization by mobile species.