Time series analyses (from approximately 18.7 to 5.8 Ma) of the oxygen isotopic composition of four shallow-dwelling planktic foraminifera (Globorotalia mayeri, Dentoglobigerina altispira, Globoquadrina baroemoenensis and Globigerinoides immaturus), one deep-dwelling planktic foraminifer (Globoquadrina venezuelana) and a benthic foraminifer (Cibicidoides spp.) from Deep Sea Drilling Project Site 289 (2206 m present day depth) are used to determine the evolution of vertical thermal structure in the western equatorial Pacific. Comparisons of composite oxygen isotopic curves, representing the surface mixed-layer, the thermocline, and deep waters reveal three distinct intervals of stability in the position and strength of the thermocline during the Miocene (approximately 18.7 to 16.1 Ma; approximately 11.1 to 9.9 Ma; and approximately 7.5 to 5.8 Ma) separated by two intervals of instability of the thermocline (approximately 16.1 to 11.1 Ma; and approximately 9.9 to 7.5 Ma). From approximately 18.7 to 16.1 Ma, vertical thermal gradients were the weakest of the Miocene interval studied and the water column was highly stable. Vertical thermal gradients strengthened between approximately 16.1 and 11.1 Ma as equatorial surface waters warmed and deep waters cooled during an inferred major growth phase of the East Antarctic ice sheet. As a consequence, the strength and position of the thermocline became highly variable. This was followed, from approximately 11.1 to 9.9 Ma, by relative climatic stability, well-defined vertical thermal gradients and a slight warming of the water column. By approximately 9.9 Ma, increasing restriction of surface water flow through the Indonesian Seaway led to the piling-up of warm surface water in the western equatorial Pacific and a deepening of the thermocline. Deep waters continued to cool and vertical thermal gradients reached a Miocene maximum by approximately 7.5 Ma. From approximately 7.5 to 5.8 Ma, vertical thermal gradients were stable and the water column became highly stratified and marked by a thick, warm surface layer and a deep, well-defined thermocline. Based upon a previous assumption that ice volume growth during the middle Miocene (approximately 16.1 to 11.1 Ma) contributed to an increase in deltaO-18 values of 0.5 to 0.7 parts-per-thousand we have estimated water column temperature changes at Site 289 between approximately 18.7 and 5.8 Ma. Surface waters are inferred to have warmed 2-degrees to 4-degrees-C between approximately 18.7 and 5.8 Ma, with about half of the warming occurring from approximately 16.1 to 11.1 Ma. Between approximately 11.1 and 9.9 Ma the entire water column warmed and from approximately 9.9 to 7.5 Ma the mixed-layer expanded and the thermocline deepened as warm waters piled-up in the western equatorial Pacific in response to the Indonesian Seaway. The net decrease of thermoclinal deltaO-18 values between approximately 11.1 and 7.5 Ma reflects an upward change in position of the deep-dwelling planktic foraminifera, Globoquadrina venezuelana, relative to the position of the thermocline as the thermocline deepened. After 7.5 Ma, relative deltaO-18 go values indicate that Globoquadrina venezuelana was a deep-dwelling, mixed-layer species. Deep waters (approximately 2400 to 2200 m) at Site 289 cooled 2-degrees to 4-degrees-C between approximately 18.7 and 5.8 Ma, with about half of the cooling occurring from approximately 16.1 to 11.1 Ma and the other half from approximately 9.9 to 7.5 Ma.