The frequency of marine heatwaves (MHWs) events has been rising globally in recent years, and this trend is expected to continue in the region off the coast of south Java Island. These oceanic extreme events may have the potential to devastate marine habitats, ecosystems and fisheries. This paper characterized MHWs off south Java from 1982 to 2019 using satellite-observed sea surface temperature. The aim of this study was to examine the dynamics of MHWs in one of Indonesia's most important fisheries hotspots, located in the southeast of the tropical Indian Ocean. We have identified two strong MHWs events in 1998 and 2016, both of which started in the austral winter months. Both events were lasted through the spring before dissipating in the early austral winter. These intense MHWs were likely related to a strong El Niño and decreased monsoon activity.

Previous studies have shown the presence of strong mesoscale eddy activities in the Indonesian Seas and their influence on the transport and water mass properties of the Indonesian Throughflow (ITF), a mean flow from the Pacific Ocean to the Indian Ocean through the Indonesian Archipelago. This study explores the effects of these eddy activities, or high‐frequency flow variability (HFFV), on residence time and pathway of the ITF by conducting Lagrangian particle tracking experiments using a velocity field from an eddy‐resolving ocean general circulation model. Particles are released at key locations in the western and eastern routes of the ITF and tracked both backward and forward in time. To assess the effects of flow variability that has a time scale longer than a day but shorter than a month, the definition of HFFV in this study, we conduct parallel experiments using daily and monthly averaged velocity fields. Particle trajectories reveal the contrasting circulation characteristics of the Sulawesi and Banda Seas. HFFV in the Sulawesi Sea (in the western route) is high, causing water to circulate longer over a broader area. The longer residence time in the Sulawesi Sea helps the upwelling of the inflowing Pacific waters, especially the intermediate water masses, to rise above 300 m at the Makassar Strait, and also has the potential to allow mixing processes to modify the water mass properties of the ITF. In contrast, HFFV is much lower in the Banda Sea and has minimal effects on the ITF.

The change in salinity of Indonesian Upper Water (IUW) in the Indian Ocean has been examined during 2004–2020 based on the Argo product. Monthly salinity fields reveal a contrast of IUW salinity changes between two time periods (2004–2013 and 2014–2020) in the outflow of Indonesian Throughflow (ITF) in the Indian Ocean. Freshening of IUW has been observed in the Indian Ocean from 2004-2013 on a basin scale. The opposite changes appear from 2014-2020, when IUW shows a general increase in salinity. The present study shows that oceanic-atmospheric processes in the Maritime Continent influence the changes in the IUW salinity in the southeastern Indian Ocean. The salinity changes are connected to the alteration of the freshwater flux in the Maritime Continent. The ITF enhances subsequent salinity transport into the southeastern Indian Ocean. Zonal atmospheric circulation strength in the tropical region is linked to the shift of the large freshwater flux in the Maritime Continent.

MHWs in the Java Sea have exhibited a statistically significant increase in frequency and duration over the period 1982–2021, with notable peaks in 1998, 2005, 2010, and 2015.Reduced latent heat lo...