Growing concern over the impacts of modern ocean acidification (OA) and interest in historical pH excursions have intensified the development of geochemical proxies for organism exposure to acidification and other components of the carbonate system. The use of carbonate structures produced by foraminifers, coccolithophores, corals, mollusks, brachiopods, echinoderms, ostracods, and fish for paleoreconstructions is an active area of study, and the resulting proxy development offers new opportunities for studying modern faunal exposures. Here we review information from field studies and laboratory experiments on carbonate system geochemical proxies in protists and metazoa. Geochemical proxy development for foraminifers and corals is most advanced; studies of fish and echinoderms are in their infancy. The most promising geochemical proxies are those with a mechanistic link to changes in seawater carbonate chemistry, such as boron isotopes (δ11B), B/Ca, and U/Ca ratios recorded in skeletal hard parts. We also discuss indirect geochemical proxies (other trace elements and carbonate polymorphs) along with their potential uses and limitations due to modification by physiological processes, precipitation rate, and degree of calcification. Proxy measurements in modern skeletal structures, otoliths, statoliths, and other hard parts could reveal environmental exposures of organisms from larval through adult stages, and could advance inferences about effects of OA (and other stressors) on survival, growth, population connectivity, and other ecological attributes. Use of geochemical proxies in live, field-collected organisms is an underutilized and underdeveloped approach to studying OA consequences, but it may offer a powerful, complementary approach to laboratory observations.

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