The Seychelles-Chagos Thermocline Ridge (SCTR) is a biologically important region of open ocean upwelling within the south west Indian Ocean (5–10°S and 45–90°E), driven by the tropical gyre. The SCTR refers to an elongated feature that joins two local minima in thermocline depth; the Seychelles Dome (SD) and Chagos Dome (CD). Entering the ocean basin from the east, the Indonesian Throughflow (ITF) has been shown to interact with the upwelling region, although the relationship between the phytoplankton bloom associated with the SCTR and the ITF are so far unexplored. Using in situ observations and remotely sensed data, the buoyancy fluxes from the ITF are shown to strongly condition surface chlorophyll-a (chl-a) concentrations over the Chagos Dome, the eastern extreme of the SCTR, at seasonal and interannual scales. Accordingly, we find a significant inverse correlation (r = −0.43) between the altimeter-derived volume transport of the ITF and the surface chl-a concentrations. This inverse correlation increases (r = −0.61) when only the 10th and 90th percentile of the ITF volume transport anomalies are considered, indicating the influence of the ITF may be overcoming other physical drivers, especially under extreme ITF events. We hypothesise that the buoyancy flux of a strong ITF input ‘caps’ the Chagos Dome with warm, less saline waters, suppressing surface phytoplankton and reducing the surface chl-a concentrations. This hypothesis is supported by a strong, significant correlation (r = 0.66) between remotely sensed surface salinity and surface chl-a over the region. This relationship is not found over the Seychelles Dome, where the ITF has a weaker direct impact over the bloom. These results suggest that the westward travel of ITF waters may condition the eastward expansion of the SCTR and, therefore, the zonal extent of the associated chl-a bloom. This happens at seasonal and interannual time-scales concomitantly with the propagation of downwelling Rossby waves, deepening the thermocline and facilitating the westward advance of ITF waters. This is visible through a combination of remotely sensed and in situ observations at depth from the RAMA mooring array at the eastern domain of the SCTR, where intrusions of warm, less saline waters, typical of ITF waters, coincide with downwelling Rossby waves deepening the thermocline. Thus, both the westward travel of ITF waters and the propagation of downwelling Rossby waves shape the eastward expansion of the SCTR and, therefore, the zonal extent of the associated surface chl-a bloom on a year-to-year basis.