The Southern Ocean hosts a large diversity of diatoms that play a major role in carbon fluxes. How the seasonal dynamics in the abundance of specific taxa in surface waters are linked to their contribution to carbon export remains, however, poorly understood. We present here synchronized observations from autonomous samplers deployed in the mixed layer (42 m) and at depth (300 m) during an entire productive season (October 2016 to March 2017) in the iron fertilized region of the central plateau of Kerguelen. Microscopic observations of surface water collected every 11 d revealed 30 different diatom taxa, each contributing to > 1% of total carbon biomass throughout the season. The synchronized sampling revealed a common pattern for diatom taxa belonging to 12 different genera, consisting, for a given taxon, in short pulses of abundance in surface waters followed by export. We explain these coupled dynamics by the formation of aggregates that are produced when a critical diatom cell abundance is reached. This control of the maximum abundance of a given diatom drives the seasonal change in the slope of the size‐class distribution of the diatom community. It further constrains the total carbon diatom biomass in a narrow range of values due to the inverse relationship between total diatom abundance and their community‐weighted mean biomass. This coupling let us conclude that aggregate formation, and the export to depth, occurs throughout the season for diatoms with different morphologies.