The sensitivities of benthic foraminiferal Mg/Ca and Li/Ca to bottom water temperature and carbonate saturation state have recently been assessed. Here we present a new approach that uses paired Mg/Ca and Li/Ca records to calculate simultaneous changes in temperature and saturation state. Using previously published records, we first use this approach to document a cooling of deep ocean waters associated with the establishment of the Antarctic ice sheet at the Eocene-Oligocene climate transition. We then apply this approach to new records of the Middle Miocene Climate Transition from ODP Site 761 to estimate variations in bottom water temperature and the oxygen isotopic composition of seawater. We estimate that the oxygen isotopic composition of seawater varied by ∼1‰ between the deglacial extreme of the Miocene Climatic Optimum and the glacial maximum following the Middle Miocene Climate Transition, indicating large amplitude variations in ice volume. However, the longer-term change between 15.3 and 12.5 Ma is marked by a ∼1°C cooling of deep waters, and an increase in the oxygen isotopic composition of seawater of ∼0.6‰. We find that bottom water saturation state increased in the lead up to the Middle Miocene Climate Transition and decreased shortly after. This supports decreasing pCO2 as a driver for global cooling and ice sheet expansion, in agreement with existing boron isotope and leaf stomatal index CO2 records but in contrast to the published alkenone CO2 records.