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Abstract Reconstructing the spatial patterns in thermocline depth is critical for understanding ocean‐atmosphere interactions. Previous foraminiferal proxies of thermocline depth focus on gradients between planktonic foraminifera living in the surface and subsurface ocean. However, both thermocline depth changes and stratification changes will impact this measure. In this study, we outline a method for reconstructing the tropical upper ocean vertical water column profile, enabling the separate assessment of thermocline depth and stratification changes. This method uses oxygen isotope data from surface and sub‐surface calcifying planktonic foraminifera (Globigerinoides ruber albus,Globorotalia tumida,Neogloboquadrina dutertrei, andPulleniatina obliquiloculata) as well as data from benthic foraminifera from a core site below the thermocline. Using newly generated and compiled oxygen isotope data from Holocene‐aged marine sediments, we construct vertical profiles at 20 core sites in the Tropical Pacific Ocean. Quantitative estimates of thermocline depth along with error ranges from Monte Carlo simulations are extracted from the reconstructed profiles. There is a strong correlation between reconstructed Holocene and climatological thermocline depth, but the East‐West contrast in the depth of the thermocline is underestimated by 30%. Incorporating benthic information in thermocline estimates results in a dramatic improvement in the reconstruction of spatial gradients in thermocline depth compared to a simpler proxy, the difference in oxygen isotope ratio between a deeper calcifying planktonic species and the surface species,G.ruber.