The seas along the Northern Coast of Papua constitute a region with complex oceanographic conditions as they are situated within the Indo-Pacific Warm Pool (IPWP). The geographical location in the southern hemisphere induces upwelling during the west monsoon season (December-January-February). Additionally, interannual phenomena such as the El Niño Southern Oscillation (ENSO) can impact the intensity of upwelling in these waters. This study aims to compare the upwelling intensity in the seas along the Northern Coast of Papua during neutral phases and ENSO phases. The main indicators of upwelling are Sea Surface Temperature (SST) and Ekman Mass Transport (EMT). Data utilized in this study include SST from GHRSST and surface wind from ASCAT. The data processing employs the monthly composite method with spatiotemporal analysis based on anomaly results derived from monthly climatology. The analysis results reveal that El Niño 2015–2016 led to an increase in upwelling intensity ranging from 1.82 to 4.00 m/s², while La Niña 2010–2011 resulted in a weakening of upwelling intensity ranging from 4.95 to 6.56 m/s² in the seas along the Northern Coast of Papua. Based on correlation and regression analysis, it can be concluded that offshore EMT significantly influences upwelling anomalies in the southeastern waters, whereas the northwestern waters are more influenced by the shifting IPWP during ENSO.