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.