The distributions of dissolved and particulate thorium isotopes (230Th and 232Th) were established in samples from the BONUS GoodHope (BGH) IPY-GEOTRACES cruise in the SE Atlantic sector of the Southern Ocean (36°S-13°E to 57°S-0°, Feb.–Mar. 2008). The distribution of total (dissolved + particulate) 232Th is dominated by the inputs from continental margins. The non-linear profiles of dissolved 230Th are interpreted as due to the southward upwelling of the isopycnal surfaces. However, total 230Th and 232Th versus salinity plots illustrate departures from binary mixing and provides evidence for non-conservative behavior of both isotopes along the section. We propose a model for total 230Th and 232Th scavenging and mixing along isopycnal surfaces. We use this model to estimate particle settling speeds and isopycnal eddy diffusion coefficients along the BGH section. Data-model comparison suggests particle settling velocities in the range of 400–700 m/y and isopycnal eddy diffusivity of the order of 2000 m2/s.