The causes for the Permian-Triassic Boundary (PTB) extinction, the largest mass extinction on record, remain enigmatic. The period is marked by large-scale volcanic eruptions and evidence for widespread ocean anoxia, which have led to suggestions that these events generated, or played a part in, the extinction. Furthermore, hypercapnia and ocean acidification caused by volcanic emissions of CO2 and CH4 have been put forward as potential kill mechanisms. We present the first PTB climate simulations in which ocean acidity is evaluated directly with a coupled climate-carbon cycle model. The experiments also address the sensitivity of ocean circulation and oxygen levels to uncertainties in paleogeography and to different bottom topographies. Modeled temperature and precipitation-evaporation are in good agreement with reconstructions and climate-sensitive sediments. There is also good agreement between modeled vegetation and reconstructed biomes. The reduction in ocean pH brought about by the increase in atmospheric CO2 is biologically significant. Aragonite saturation levels are low enough to make the whole ocean unsuitable to aragonitic species, and large areas of the ocean become unsaturated in relationship to calcite. No general bottom anoxia is reproduced. Modeled deep ocean O2 concentrations are not significantly impacted by changes in paleogeography and bathymetry, an indication that in our model a change in ocean dynamics resulting from climate warming is not sufficient by itself to generate widespread anoxic conditions during the period.