The Pacific Ocean (PO) greatly influences the Indonesian sea, plays a crucial role in global climate and ocean circulation, and connects to the Indian Ocean (IO). Previous research has examined the Pacific Ocean’s influence, but the roles of eddies and primary productivity in marine ecosystems during the ENSO response within the Indonesian Throughflow (ITF) in the Halmahera Sea (HS) remain unclear. This study utilizes satellite data to analyze the spatiotemporal patterns of various oceanographic parameters with the ITF during ENSO events from 2009 to 2020. The analysis incorporates satellite-derived SST, SSH, SWH, Chl-a, zooplankton variability, and volume transport. Analysis of SST and SSH variability shows the influence of SWH. The EOF analysis reveals that SSH and SST variability are impacted by ENSO events, with notable fluctuations observed in 2010–2011 and 2015–2016. The EKE divergence is higher during La Niña than El Niño events. The volume transport is strongest at depths of 100–150 m during El Niño and 50–100 m during La Niña, with interannual variations ranging from −0.709 ± 1.394 Sv in the 0–50 m layer, decreasing with depth. Our findings show different patterns for Chl-a, SST, and SSS during the ENSO events.
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