The internal development of the tropical West Pacific Warm Pool and its interaction with high latitude ocean regions on geological timescales is only poorly constrained. Based on two newly recovered sediment cores from the southeastern margin of the West Pacific Warm Pool (northern and southern Manihiki Plateau), we provide new aspects on the dynamically interacting ocean circulation at surface, subsurface, thermocline, and deep thermocline levels during the Pleistocene (~ 2.5–0.5 Ma). Notably, the variability of thermocline and deep thermocline (~ 150–400 m water depth) foraminiferal Mg/Ca-based temperatures with up to ~ 6 °C amplitude variations exceeds those at shallower depths (down to ~ 120 m) with only ~ 2–3 °C temperature variations. A major gradual reorganization of the West Pacific Warm Pool oceanography occurred during the transitional time period of ~ 1.7–1.35 Ma. Prior to ~ 1.7 Ma, pronounced meridional and latitudinal gradients in sea-surface to subsurface ocean properties point to the eastward displacement of the West Pacific Warm Pool boundaries, with the South Pacific Convergence Zone being shifted further northeastward across Manihiki Plateau. Simultaneously, the low amplitude variations of thermocline and deep thermocline temperatures refer to an overall deep and stable thermocline. The meridional and zonal gradients in sea-surface and subsurface ocean properties within the West Pacific Warm Pool reveal a pronounced change after 1.5 Ma, leading to a more southward position of the warm South Pacific Convergence Zone between ~ 1.35–0.9 Ma and ~ 0.75–0.5 Ma. Synchronous to the changes in the upper ocean, the deeper water masses experienced high amplitude variations in temperature, most prominently since ~ 1.5 Ma. This and the dynamically changing thermocline were most likely associated to the impact of southern-sourced mode waters, which might have developed coincidently with the emergence of the East Pacific Cold Tongue and high latitude sea-surface cooling.