Ocean acidification results in co-varying inorganic carbon system variables. Of these, an explicit focus on pH and organismal acid–base regulation has failed to distinguish the mechanism of failure in highly sensitive bivalve larvae. With unique chemical manipulations of seawater we show definitively that larval shell development and growth are dependent on seawater saturation state, and not on carbon dioxide partial pressure or pH. Although other physiological processes are affected by pH, mineral saturation state thresholds will be crossed decades to centuries ahead of pH thresholds owing to nonlinear changes in the carbonate system variables as carbon dioxide is added. Our findings were repeatable for two species of bivalve larvae could resolve discrepancies in experimental results, are consistent with a previous model of ocean acidification impacts due to rapid calcification in bivalve larvae, and suggest a fundamental ocean acidification bottleneck at early life-history for some marine keystone species.