It has been reported that the sea level falls in the tropical Southwest Indian Ocean (SWIO) from the 1960s to the early 2000s. However, a rising trend of 4.05 ± 0.56 cm/decade has occurred during the recent two decades with our analysis showing that manometric sea level contributes 41% to this sea level rise. 30% of this rise is due to steric sea level (SSL) change in the upper 2,000 m with SSL rise in the upper 300 m of secondary importance. Conversely, thermal expansion below the thermocline (300–2,000 m), likely caused by water mass spread from the Southern Ocean, induces major contribution to SSL changes. Compared to existing studies demonstrating the contribution of thermal variations above the thermocline to sea level variability in the tropical SWIO, this study emphasizes the importance of ocean mass and deeper ocean changes in a warming climate.