Stable isotope and elemental measurements were conducted on foraminifera from a sequence of calcareous pelagic ooze at Ocean Drilling Program Site 1209 to document the thermal evolution of the North Pacific water column over Shatsky Rise and to address long-standing questions about the nature of oceanic circulation in the early Paleogene. A major change in seasonality and water column structure in the early Eocene marks a change in tropical Pacific climate and circulation just prior to the early Eocene climatic optimum. Subsequent long-term cooling is interrupted by a transient positive δ18O excursion identified in planktonic and benthic foraminifera during the late early Eocene that is interpreted as evidence for ephemeral formation of deep water from a low-latitude, saline source. Paired analysis of benthic Mg/Ca and δ18O was undertaken to assess the relative contribution of temperature and seawater oxygen isotope composition to the benthic δ18O record. Stratigraphic trends of benthic δ18O and Mg/Ca decouple during two intervals in the early Eocene and early middle Eocene. Although variable seawater δ18O is the most likely candidate to explain decoupling of benthic δ18O and Mg/Ca, it is difficult to argue for substantial change in continental ice volume during a presumably ice-free interval of time.