Sedimentary specimens of the planktonic foraminifera Globorotalia inflata can provide much needed information on subsurface conditions of past oceans. However, interpretation of its geochemical signal is complicated by possible effects of cryptic diversity and encrustation. Here we address these issues using plankton tow and sediment samples from the western South Atlantic, where the two genotypes of G. inflata meet at the Brazil-Malvinas Confluence Zone. The 18O and δ13C of encrusted specimens from both genotypes from a core within the confluence zone are indistinguishable. However, we do find a large influence of encrustation on δ18O and Mg/Ca. Whereas crust Mg/Ca ratios are at all locations lower than lamellar calcite, the crust effect on δ18O is less consistent in space. Plankton tows show that encrusted specimens occur at any depth and that even close to the surface crust Mg/Ca ratios are lower than in lamellar calcite. This is inconsistent with formation of the crust at lower temperature at greater depth. Instead we suggest that the difference between the crust and lamellar calcite Mg/Ca ratio is temperature-independent and due to the presence of high Mg/Ca bands only in the lamellar calcite. The variable crust effect on δ18O is more difficult to explain, but the higher incidence of crust free specimens in warmer waters and the observation that a crust effect is clearest in the confluence zone, hint at the possibility that the difference reflects advective mixing of specimens from warmer and colder areas, rather than vertical migration.