Human driven changes such as increases in oceanic CO2, global warming, petroleum hydrocarbons and heavy metals may negatively affect the ability of marine calcifiers to build their skeletons/shells, especially in polar regions. We examine spatio-temporal variability of skeletal Mg-calcite in shallow water Antarctic marine invertebrates using bryozoan and spirorbids as models in a recruitment experiment of settlement tiles in East Antarctica. Mineralogies were determined for 754 specimens belonging to six bryozoan species (four cheilostome and two cyclostome species) and two spirorbid species from around Casey Station. Intra- and interspecific variability in wt% MgCO3 in calcite among most species was the largest source of variation overall. Therefore, the skeletal Mg-calcite in these taxa seem to be mainly biologically controlled. However, significant spatial variability was also found in wt% MgCO3 in calcite, possibly reflecting local environment variation from sources such as freshwater input and contaminated sediments. Species with high-Mg calcite skeletons (e.g. Beania erecta) could be particularly sensitive to multiple stressors under predictions for near-future global ocean chemistry changes such as increasing temperature, ocean acidification and pollution.