As the ocean undergoes acidification, marine organisms will become increasingly exposed to reduced pH, yet variability in many coastal settings complicates our ability to accurately estimate pH exposure for those organisms that are difficult to track. Here we present shell-based geochemical proxies that reflect pH exposure from laboratory and field settings in larvae of the mussels Mytilus californianus and M. galloprovincialis. Laboratory-based proxies were generated from shells precipitated at pH 7.51 to 8.04. U/Ca, Sr/Ca, and multielemental signatures represented as principal components varied with pH for both species. Of these, U/Ca was the best predictor of pH and did not vary with larval size, with semidiurnal pH fluctuations, or with oxygen concentration. Field applications of U/Ca were tested with mussel larvae reared in situ at both known and unknown pH conditions. Larval shells precipitated in a region of greater upwelling had higher U/Ca, and these U/Ca values corresponded well with the laboratory-derived U/Ca-pH proxy. Retention of the larval shell after settlement in molluscs allows use of this geochemical proxy to assess ocean acidification effects on marine populations.