Within the Subantarctic Mode Water (SAMW) density level, we study temporal changes in salinity, nutrients, oxygen and TTD (Transit Time Distribution) ages in the western (W) and eastern (E) subtropical gyre of the Indian Ocean (IO) from 1987 to 2002. Additionally, changes in Total Alkalinity (TA) and Dissolved Inorganic Carbon (DIC) are evaluated between 1995 and 2002. The mechanisms behind the detected changes are discussed along with the results from a hindcast model run (Community Climate System Model). The increasing salinity and decreasing oxygen trends from 1960 to 1987 reversed from 1987 to 2002 along the gyre. In the W-IO a decreasing trend in TTD ages points to a faster delivery of SAMW, thus less biogenic matter remineralization, explaining the oxygen increase and noisier nutrients decrease. In the E-IO SAMW, no change in TTD ages was detected, therefore the trends in oxygen and inorganic nutrients relate to changes in the Antarctic Surface Water transported into the E-IO SAMW formation area. In the W-IO between 1995 and 2002, the DIC increase is equal or even less than the anthropogenic input as the reduction in remineralization contributes to mask the increasing trend. In the E-IO between 1995 and 2002, DIC decreases slightly despite the increase in the anthropogenic input. Differences in the preformed E-IO SAMW conditions would explain this behavior. Trends in the W and E IO SAMW are decoupled and related to different forcing mechanisms in the two main sites of SAMW formation in the IO, at 40°S–70°E and 45°S–90°E, respectively.