Global oceans are known to have alternated between aragonite and calcite seas. These oscillations reflect changes in the Mg/Ca ratios of seawater that control biomineralization and the composition of marine carbonates, and are thought to be caused mainly by the time dependence of crustal accretion at mid-ocean ridge crests and the associated high-temperature mid-ocean ridge fluid flux. Here we use global ocean basin reconstructions to demonstrate that the fluctuations in hydrothermal ocean inputs are instead caused by the gradual growth and destruction of mid-ocean ridges and their relatively cool flanks during long-term tectonic cycles, thus linking ocean chemistry to off-ridge low-temperature hydrothermal exchange. Early Jurassic aragonite seas were a consequence of supercontinent stability and a minimum in mid-ocean ridge length and global basalt alteration. The breakup of Pangea resulted in a gradual doubling in ridge length and a 50% increase in the ridge flank area, leading to an enhanced volume of basalt to be altered. The associated increase in the total global hydrothermal fluid flux by as much as 65%, peaking at 120 Ma, led to lowered seawater Mg/Ca ratios and marine hypercalcification from 140 to 35 Ma. A return to aragonite seas with preferential aragonite and high-Mg calcite precipitation was driven by pronounced continental dispersal, leading to progressive subduction of ridges and their flanks along the Pacific rim.