In the Southern Ocean, the silicon (Si) biogeochemical cycle is dominated by processes such as the supply of Si into the surface waters, Si uptake into diatom frustules, and their subsequent dissolution and export. Due to the incomplete assimilation of the silicic acid pool (DSi) and isotopic fractionation during silicification, the Si isotopic composition (δ³⁰Si) of biogenic silica (BSi) is closely linked to the degree of Si utilization in the mixed layer (ML). In this study, we combined modelling approaches and seasonal sediment trap records of δ³⁰Si of exported BSi to investigate the magnitude, timing, and isotopic composition of the flux of siliceous particles transferred from the surface to the deep ocean. We implemented a box model to describe the temporal evolution of DSi and BSi concentrations and δ³⁰Si in the ML and at depth. The model allows us to quantify fluxes of Si in and out of the ML associated with export, dissolution, and mixing. It highlights that the time‐integrated δ³⁰Si of exported BSi measured in the sediments reflects the extent of DSi consumption at the time when net BSi production and diatom accumulation are maximal in the ML and confirms that the δ³⁰Si of diatoms is a reliable proxy for past Si utilization.