Long-term ocean deoxygenation could lead to decline biological productivity and alter biogeochemical cycles. Ocean warming contributions to ocean deoxygenation are reasonably understood, however, there is a challenge to reveal the gaps about other modifying factors to explain different regional patterns and predicts the condition in the coming century. This study aimed to identify the deoxygenation areas in the eastern Indonesian waters, understand the variability of physical and chemical parameters as the deoxygenation drivers, and investigate the correlation between parameters. In-situ and satellite-derived data from 1995 to 2020 were analyzed with statistical methods and remote sensing techniques to enhance deoxygenation measures in higher spatial and temporal resolutions. Our findings revealed that significant deoxygenation was detected around the Arafura Sea. The oxygen minimum zone extended at 133.5° – 136.8° E in the depth of 350 – 1,000 meters, with less than 20 mmol/m3 of dissolved oxygen concentration. Nitrate, phosphate, and temperature were identified to have a strong reversed relationship with the oxygen concentration in the study area. This study also developed multiple regression model algorithms to estimate the oxygen concentration in specified depths.