The Neoproterozoic Earth underwent at least two severe glaciations, each extending to low paleomagnetic latitudes and punctuating warmer climates. The two widespread older and younger Cryogenian glacial deposits in Namibia are directly overlain by cap carbonates deposited under inferred periods of high atmospheric carbon dioxide concentrations. Oceanic uptake of carbon dioxide decreases ocean pH; here we present a record of Cryogenian interglacial ocean pH, based on boron (B) isotopes in marine carbonates. Our data suggest a largely constant ocean pH and no critically elevated pCO2 throughout the older postglacial and interglacial periods. In contrast, a marked ocean acidification event marks the younger deglaciation period and is compatible with elevated postglacial pCO2 concentration. Our data are consistent with the presence of two panglacial climate states in the Cryogenian, but indicate that each had its own distinct environmental conditions.