Hanifaru Bay, in Baa Atoll, Maldives, is globally recognised for hosting the largest known feeding aggregations of reef manta rays (Mobula alfredi). These aggregations are spatially and temporally discrete, often associated with flood tides, and are thought to result from hydrodynamic processes that elevate zooplankton concentrations. This study investigates the role of flow-topography interactions, specifically around the small headland-like feature in the bay’s inlet (the ‘nodule’), in creating conditions conducive to these feeding events. A Delft3D hydrodynamic model of Baa Atoll was developed to simulate tidal flows within the bay, with high-resolution mesh focusing on Hanifaru Bay. Calibration and validation against in situ observations ensured the model reliably captured tidal dynamics. Results indicate that a retentive eddy forms behind the nodule during the flood tide, consistent with the timing of manta ray feeding events. This closed-core eddy retains zooplankton, allowing for their accumulation within the bay. By contrast, during the ebb tide, flow-through conditions prevent zooplankton aggregation.