Records from South America show that modern ENSO (El Nino-Southern Oscillation) did not exist 7000 cal yr B.P. and has developed progressively since then. There has been little information available on oceanic conditions in the eastern equatorial Pacific (EEP) to constrain explanations for ENSO onset. We report quantitative observations on thermocline and mixed-layer conditions in the EEP during ENSO start up. We found important changes in both the thermocline and the mixed layer, indicating increased upwelling of cooler waters since 7000 cal yr B.P. This resulted from change in the source and/or properties of waters supplying the Equatorial Undercurrent, which feeds upwelling along the equator and the Peru margin. Modeling shows that ENSO is sensitive to subsurface conditions in the eastern equatorial Pacific and that the changes in the thermocline we observed were driven by extratropical processes, giving these a role in conditioning the development of ENSO. This is in contrast to models that call for control of equatorial Pacific oceanography by tropical processes only. These infer stronger upwelling and cooler surface waters for the EEP during the mid-Holocene, which is not supported by our results.