The South‐East Madagascar Bloom, one of the most compelling biogeochemical features of the Indian Ocean, occurs sporadically during austral summer in the oligotrophic waters south‐east of Madagascar, where it can cover up to 1% of the global ocean surface area. Its spatial extension and its timing are highly variable. A high‐resolution biophysical model is used to investigate a previous hypothesis that the onset of a particular circulation of the South‐East Madagascar Current advects fresher and nutrient‐rich waters eastward, feeding the bloom. The model is able to reproduce an intermittent phytoplankton bloom with large spatial variability but in the subsurface layers, as well as the presence of an irregular retroflection of the South‐East Madagascar Current. The simulated bloom occurs within a shallow stratified mixed layer, with fresher waters at the surface, parallel to the water mass in an observed bloom. The model results suggest, from a nutrient flux analysis, that horizontal advection of low‐salinity nutrient‐rich Madagascan coastal waters can indeed trigger a phytoplankton bloom. The coupled model is also able to resolve a bloom that is atmospherically forced by cyclonic activity.