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We document the waxing and waning of a ‘proto-Western Pacific Warm Pool’ and Equatorial Undercurrent (EUC) based on a study of multi-species planktic foraminiferal isotope ratios and census data spanning the 13.2-5.8 Ma interval at ODP Site 806 in the western equatorial Pacific (WEP). We hypothesize that the presence or absence of a proto-warm pool in the WEP, caused by the progressive tectonic constriction of the Indonesian Seaway and modulated by sea level fluctuations, created El Niño/La Niña-like alternations of hydrographic conditions across the equatorial Pacific during the late Miocene. This hypothesis is supported by the general antithetical relationship observed between carbonate productivity and preservation in the western and eastern equatorial Pacific, a phenomenon caused by these alternating ocean-climate states in the modern ocean. The two-step development and intensification of a proto-warm pool 11.6-9.6 Ma coincides with ice sheet expansion associated with Miocene isotope events Mi5 and Mi6, resulting in a cumulative sea level fall of 50 m and production of Northern Component Water. It also marks the initiation of a more modern equatorial current system as La Niña-like conditions became established across the tropical Pacific. This situation sustained carbonate and silica productivity in the eastern equatorial Pacific (EEP) at a time when carbonate preservation sharply declined in the Caribbean. Proto-warm pool weakening after 10 Ma may have contributed to the nadir of a similar ‘carbonate crash’ in the EEP. Decay of the proto-warm pool and resultant El Niño-like conditions brought higher productivity to the WEP, particularly 9.0-8.8 Ma coincident with a major perturbation in tropical nannofossil assemblages. This interval of increased productivity records the initial phase of the widespread ‘biogenic bloom’. Resurgence of a later proto-warm pool in the WEP 6.5-6.1 Ma may have spurred renewed La Niña-like conditions, which contributed to a strong late phase of the ‘biogenic bloom’ in the EEP.