The bottom water conditions in the Central South Pacific (CSP) and associated changes in the Lower Circumpolar Deep Water (LCDW) and Antarctic Bottom Water (AABW) under warmer-than-present conditions need to be better understood. These water masses transfer their properties to the major ocean basins. We analyzed Late Miocene to Early Pliocene (5.6–3.6 Ma) marine sediment core sections from the CSP for benthic foraminifera, ice rafted debris (IRD), Ostracoda, planktic foraminifera Orbulina universa abundance, and organic geochemical proxies to assess the bottom water characteristics under warmer-than-present day conditions. A significant increase in IRD abundance between 5.3 and 4.9 Ma marks the Early Pliocene warm phase. The benthic foraminiferal assemblages indicate shifts in bottom water conditions over time in the CSP region. Between 5.6 and 5.3 Ma, predominantly oxygenated bottom water with moderate organic matter flux prevailed. This shifted to suboxic conditions with increased organic matter flux from 5.3 to 4.9 Ma. Subsequently, between 4.9 and 4.4 Ma, bottom water conditions alternated frequently between oxic and suboxic states. Enhanced bottom water formation and inflow of LCDW and AABW in the CSP during 4.4–4.0 Ma promoted oxygenated conditions, accompanied by low organic export flux. However, sluggish bottom water circulation from 4.0 to 3.6 Ma reverted to suboxic conditions, associated with increased carbon burial. Notably, productivity peaked intermittently between 5.3 and 3.6 Ma, as indicated by the occurrence of suboxic species assemblages and increase in the abundance of Orbulina universa, benthic microfauna (ostracods), and other paleoproductivity indicators.