The concentrations of rare earth elements (REEs) in seawater display systematic variations related to weathering inputs, particle scavenging and water mass histories. Here we investigate the REE concentrations of water column profiles in the Atlantic sector of the Southern Ocean, a key region of the global circulation and primary production. The data reveal a pronounced contrast between the vertical profiles in the Antarctic Circumpolar Current (ACC) and those south of the ACC in the Weddell Gyre (WG). The ACC profiles exhibit the typical increase of REE concentrations with water depth and a change in the shape of the profiles from near linear for the light REEs to more convex for the heavy REEs. In contrast, the WG profiles exhibit high REE concentrations throughout the water column with only the near surface samples showing slightly reduced concentrations indicative of particle scavenging. Seawater normalised REE patterns reveal the strong remineralisation signal in the ACC with the light REEs preferentially removed in surface waters and the mirror image pattern of their preferential release in deep waters. In the WG the patterns are relatively homogenous reflecting the prevalence of well-mixed Lower Circumpolar Deep Water (LCDW) that follows shoaling isopycnals in the region. In the WG particle scavenging of REEs is comparatively small and limited to the summer months by light limitation and winter sea ice cover. Considering the surface water depletion compared to LCDW and that the surface waters of the WG are replaced every few years, the removal rate is estimated to be on the order of 1 nmol m− 3 yr− 1 for La and Nd. The negative cerium anomalies observed in deep waters are some of the strongest found globally with only the deepest waters in parts of the Pacific having stronger anomalies. These deep waters have been isolated from fresh continental REE inputs during their long journey through the abyssal Indo-Pacific Ocean, which suggests that the high REE concentrations found in the ACC and WG reflect contributions from old deep waters.