Southern Ocean biogeochemical processes have an impact on global marine primary production and global elemental cycling, e.g. by likely controlling glacial-interglacial <i>p</i>CO₂ variation. In this context, the natural silicon isotopic composition (&delta;³⁰Si) of sedimentary biogenic silica has been used to reconstruct past Si-consumption:supply ratios in the surface waters. We present a new dataset in the Southern Ocean from a IPY-GEOTRACES transect (Bonus-GoodHope) which includes for the first time summer &delta;³⁰Si signatures of suspended biogenic silica (i) for the whole water column at three stations and (ii) in the mixed layer at seven stations from the subtropical zone up to the Weddell Gyre. In general, the isotopic composition of biogenic opal exported to depth was comparable to the opal leaving the mixed layer and did not seem to be affected by any diagenetic processes during settling, even if an effect of biogenic silica dissolution cannot be ruled out in the northern part of the Weddell Gyre. We develop a mechanistic understanding of the processes involved in the modern Si-isotopic balance, by implementing a mixed layer model. We observe that the accumulated biogenic silica (sensu Rayleigh distillation) should satisfactorily describe the &delta;³⁰Si composition of biogenic silica exported out of the mixed layer, within the limit of the current analytical precision on the &delta;³⁰Si. The failures of previous models (Rayleigh and steady state) become apparent especially at the end of the productive period in the mixed layer, when biogenic silica production and export are low. This results from (1) a higher biogenic silica dissolution:production ratio imposing a lower net fractionation factor and (2) a higher Si-supply:Si-uptake ratio supplying light Si-isotopes into the mixed layer. The latter effect is especially expressed when the summer mixed layer becomes strongly Si-depleted, together with a large vertical silicic acid gradient, e.g. in the Polar Front Zone and at the Polar Front.