The fractionation of silicon (Si) stable isotopes by biological activity in the surface ocean makes the stable isotope composition of silicon (δ30Si) dissolved in seawater a sensitive tracer of the oceanic biogeochemical Si cycle. We present a high-precision dataset that characterizes the δ30Si distribution in the deep Atlantic Ocean from Denmark Strait to Drake Passage, documenting strong meridional and smaller, but resolvable, vertical δ30Si gradients. We show that these gradients are related to the two sources of deep and bottom waters in the Atlantic Ocean: waters of North Atlantic and Nordic origin carry a high δ30Si signature of ≥+1.7‰ into the deep Atlantic, while Antarctic Bottom Water transports Si with a low δ30Si value of around +1.2‰. The deep Atlantic δ30Si distribution is thus governed by the quasi-conservative mixing of Si from these two isotopically distinct sources. This disparity in Si isotope composition between the North Atlantic and Southern Ocean is in marked contrast to the homogeneity of the stable nitrogen isotope composition of deep ocean nitrate (δ15N-NO3). We infer that the meridional δ30Si gradient derives from the transport of the high δ30Si signature of Southern Ocean intermediate/mode waters into the North Atlantic by the upper return path of the meridional overturning circulation (MOC). The basin-scale deep Atlantic δ30Si gradient thus owes its existence to the interaction of the physical circulation with biological nutrient uptake at high southern latitudes, which fractionates Si isotopes between the abyssal and intermediate/mode waters formed in the Southern Ocean.