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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, and Pulleniatina 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. Plain Language Summary: The thermocline is a layer of the ocean where temperature changes rapidly, and the depth of this layer is related to many climatic phenomena. Understanding where and when this layer was deeper and shallower in the past is important to our overall understanding of the climate system. We outline a novel method to reconstruct the thermocline with microscopic shells collected from the sea floor. Our method can reconstruct the changes we see across the Pacific today and also recreate the changes found between the last ice age and today. Key Points: We show a novel method for reconstructing the upper water column using oxygen isotope measurements on multiple species of foraminiferaThis method can be used to quantitatively reconstruct spatial and temporal changes in thermocline depthIf a simple differencing method is preferred, thermocline depth can be most accurately reconstructed using subsurface species only [ABSTRACT FROM AUTHOR]