The dissolved oxygen (DO) decrease in the ocean is a notable issue because of its potential impacts on marine biogeochemical cycles and ecosystem services. Satellite remote sensing application to support in-situ measurement is a time and cost-saving on wide scales DO monitoring. This study aims to determine the DO variability from 1993 to 2020, identify the potential areas to experience deoxygenation, and investigate the correlation between DO and other ocean parameters in Indonesian seas. The validation between in-situ and satellite-derived DO shows the determination coefficient of 0.73, indicating the satellite dataset reliability for the entire analysis. The multiple regression analysis among the long-term satellite-derived ocean parameters shows that the in-situ DO can be estimated by the combination of the potential temperature, total chlorophyll-a, and salinity. The potential temperature was statistically identified as the parameter with the highest correlation and influence on DO. The results of DO variability analysis show the overall decreasing trend with significant decreases in 1998, 2010, and 2016. There is a distinct difference in DO’s seasonal patterns in the southwestern and northeastern regions. The potential of ocean deoxygenation is detected in western Sumatra waters and the Arafura Sea at the 200–1,000 meters depth.