We explore the relationship between atmospheric O2 and CO2 evolution and seawater chemistry, with particular focus on the CO2–carbonic acid system and ocean ventilation, over the Phanerozoic Eon using a coupled biogeochemical Earth system model (MAGic). This model describes the biogeochemical cycles involving the major components of seawater (Ca, Mg, Na, K, Cl, SO4, CO2HCO3CO3), as well as components (O2, Fe, P, organic C, reduced S) central to long-term ecosystem productivity. The MAGic calculations show that the first-order input fluxes from weathering of continental rocks of Ca, Mg, and dissolved inorganic carbon (DIC) to the ocean varied in a cyclical manner over the Phanerozoic. The cyclicity is mainly the result of the impact of changing atmospheric CO2 levels, and hence temperature and runoff, on these fluxes, reflecting the nature of hothouse (greenhouse, high CO2 and warm) versus icehouse (low CO2, cool, and continental glaciation) conditions during the Phanerozoic. Uptake of DIC by seafloor basalt–seawater reactions also varied in a corresponding fashion to the weathering fluxes. The fluxes of Ca, Mg, DIC and other seawater constituents removed in oceanic sinks were also calculated and hence with calculated inputs and outputs of seawater constituents, the changes in seawater chemistry through Phanerozoic time could be obtained. Seawater pH increased irregularly during the Phanerozoic from just above 7 in the Cambrian Period, approaching modern average values in the most recent several millions of years. Calcite saturation state also increased with decreasing age. Both pH and calcite saturation state trends exhibited a cyclic overprint of hothouse and icehouse environmental conditions. Dissolved sulfate changed in a cyclical manner reflecting mainly variations in weathering and accretion rates and redox conditions, whereas dissolved potassium exhibited little variation in concentration.Using our “standard” model results for the chemistry of seawater and changes in atmospheric CO2 and O2 as the basis for a series of sensitivity experiments, we vary the ventilation rate of the global ocean, and quantify the resulting changes in terms of processes such as net primary production, organic carbon burial and oxidation, pyrite weathering, and sulfate reduction. We use these preliminary results to discuss how changes in ocean ventilation affect atmospheric CO2 and O2, and in turn exert changes in the sulfur, organic carbon, and inorganic carbon systems. We postulate that periods of slow plate accretion rates, associated with lower atmospheric CO2, vigorous deep water formation, cooler, drier climatic conditions and greater poleward temperature gradients are more likely to be associated with a strong thermohaline circulation, and thus “enhanced” global ocean mixing. Conversely, periods of higher accretion rates, higher CO2, higher average global temperatures with more equable poleward gradients, and higher sea levels resulting in extensive continental inundation, would be more likely to be coincident with times of reduced mixing of the global ocean. It is important to recognize that the scale of these changes depends on how major tectonic cycles (controlling chemical weathering, CO2 and temperature) in turn affect nutrient supply, global ocean productivity, and global ocean thermohaline circulation. The key to elucidating these changes lies in an understanding of the relationship between long-term tectonic evolution, which leads to changes in climate, sea level, and the global distribution of continental landmasses and the sedimentary environments they host, and the circulation of the global ocean.