Ocean acidification, driven by rising atmospheric CO₂, threatens the ability of corals to build their skeletons by reducing their capacity to maintain an elevated pH at the calcification site (pH_cf), a process essential for calcium carbonate precipitation. Boron isotopes have commonly been used to show that the response of pH_cf to ocean acidification is highly species-specific. However, the physiological mechanisms underlying this variability remain poorly understood. Recently, lithium (Li) isotopes have been used to trace the activity of ionic transport involved in cellular pH regulation and calcification (e.g. H⁺, Na⁺and Ca²⁺), and may therefore help resolve these mechanisms. Here, we investigate multiple coral species from Tutum Bay (Papua New Guinea), a natural CO₂ seep system creating pH gradients (mean pH_T = 7.66 at seeps vs. 8.01 at control sites) analogous to future ocean acidification scenarios. Our results show a relationship between seawater pH, calcifying fluid chemistry, and lithium isotopic composition. Corals exposed to low seawater pH exhibit significantly altered δ⁷Li values relative to colonies from the control site, with some species becoming enriched in ⁷Li (up to 2‰) as pH_cf declines. This isotopic shift is consistent with reduced efficiency of Na⁺/H⁺ exchangers (NHEs), active transporters that preferentially incorporate the lighter ⁶Li isotope under optimal conditions but may become less effective under elevated proton concentrations. By linking Li isotopes to calcifying-fluid chemistry, these results provide geochemical evidence that ocean acidification may disrupt ionic regulation in corals and that Li isotopes can help to resolve biogeochemical controls of carbonate-systems.