The Southern Ocean plays a pivotal role in the control of atmospheric CO₂ levels, via both physical and biological sequestration processes. The biological carbon transfer to the ocean interior is tightly coupled to the availability of other elements, especially iron as a trace-limiting nutrient and dissolved silicon as the mineral substrate that allows diatoms to dominate primary production. Importantly, variations in the silicon cycling are large but not well understood. Here we use δ³⁰Si measurements to track seasonal flows of silica to the deep sea, as captured by sediment trap time series, for the three major zones (Antarctic, AZ; Polar Frontal, PFZ; and Sub-Antarctic, SAZ) of the open Southern Ocean. Variations in the exported flux of biogenic silica (BSi) and its δ³⁰Si composition reveal a range of insights, including that (i) the sinking rate of BSi exceeds 200 m d⁻¹ in summer in the AZ yet decreases to very low values in winter that allow particles to remain in the water column through to the following spring, (ii) occasional vertical mixing events affect the δ³⁰Si composition of exported BSi in both the SAZ and AZ, and (iii) the δ³⁰Si signature of diatoms is well conserved through the water column despite strong BSi and particulate organic carbon (POC) attenuation at depth and is closely linked to the Si consumption in surface waters. With the strong coupling observed between BSi and POC fluxes in PFZ and AZ, these data provide new constraints for application to biogeochemical models of seasonal controls on production and export.