Deep-sea corals are a useful archive of thermocline, intermediate, and deep waters in past oceans. However, application of traditional oceanographic tracers to deep-sea corals remains a challenge due to our insufficient understanding of their “vital effects”. Deep-sea corals are ideal test organisms to study the mechanism underlying vital effects generally, due to the large tracer gradients in individual corals living under relatively constant environmental conditions. Lessons learned from these corals might apply to other scleractinia and to marine calcifiers more generally. Here we present stable isotope, minor and trace metal (Me/Ca ratios) data in a suite of modern Desmophyllum dianthus specimens, collected over multiple spatial scales in individual corals (bulk, micromill, SIMS, NanoSIMS), with multi-proxy analyses made on the same material whenever possible. Spatially coherent Me/Ca correlations are observed in the fibrous aragonite of individual corals, including positive correlations between Mg/Ca, Li/Ca and B/Ca, as well as negative correlations between Mg/Ca and Sr/Ca, consistent with previous studies. We also for the first time document strong correlations between the isotopic (δ18O and δ13C) and elemental compositions of the skeletons, most notably a negative correlation between δ18O and Mg/Ca. The centers of calcification (COCs) in the coral skeletons show distinct tracer correlations from the aragonite fibers that possibly reflect a more complicated formation mechanism. We interpret the spatially coherent tracer correlations in deep-sea corals with a numerical model of coral calcification previously developed for stable isotopes that considers the role of the enzyme carbonic anhydrase in the calcification processs. With the carbonate chemistry in the model constrained by the stable isotope data, we are able to explain the observed Me/Ca correlations as well as their range of variability, as a result of internal pH elevation in the extracellular calcifying fluid (ECF) of the corals with limited Ca-pumping through the calicoblastic membrane. In particular, the positive Mg/Ca–B/Ca correlation in the fibrous aragonite suggests a borate (B(OH)4–) substitution for carbonate ion (CO32–) incorporation mechanism in biogenic aragonite. We also suggest the growth rate dependence of the incorporation of minor and trace elements based conceptually on an ion-by-ion growth model may help explain the absolute Me/Ca values in biogenic aragonites. Finally, we generally find more limited tracer variability in corals from undersaturated seawater compared to their counterparts from supersaturated conditions, suggesting a limit to their internal pH elevation in response to this environmental stress. Understanding the biomineralization mechanisms underlying the vital effects is important for better use of these tracers for paleoceanographic applications, and may shed light on the response of marine calcification to future ocean acidification.