The Impact of the Mindanao and Halmahera Eddies on the Indonesian Throughflow Seasonal and Interannual Variations

Abstract The Mindanao eddy (ME) and Halmahera eddy (HE) are major mesoscale systems in the Indonesian Throughflow (ITF) source region, yet their interactive influence on ITF transport remains unclear. Using GLORYS12V1 reanalysis data (1993–2020) from the Copernicus Marine Environment Monitoring Service and a Self‐Organizing Map (SOM) approach, this study classifies the ME–HE coevolution into four typical flow patterns and explores their seasonal and interannual impacts on ITF transport. Results show that the cooperative pattern of ME's eastward expansion with HE's southeast retreat (Pattern 1) minimizes Makassar Strait transport by weakening the Mindanao Current (MC) intrusion into Sulawesi Sea. Conversely, Patterns 2–4 enhance ITF transport through different mechanisms: Pattern 2 involves a weakened ME and northward‐shifted HE; Pattern 3 features a strong northwestward HE that compresses the MC and yields the strongest transport; Pattern 4 represents a transitional configuration with enhanced HE and moderate ME strength. Seasonal patterns shifts are mainly controlled by local wind stress and Ekman pumping. Strong northeast monsoons in boreal winter favor Pattern 1 and weak ITF, while boreal summer southwest winds support Patterns 2–4 and strong ITF. On interannual timescale, ENSO‐driven wind anomalies and westward‐propagating Rossby waves jointly modulate eddy evolution through sea surface height anomalies. El Niño event promotes Pattern 1, while La Niña event favors Pattern 3. Patterns 2 and 4 serve as transitional states due to the asynchronous responses of the ME and HE to ENSO forcing. Additionally, the confluence of the South China Sea Throughflow and MC further modulates ITF transport.