Data from Ocean Drilling Program Site 1263 on Walvis Ridge in SE Atlantic include barite accumulation rates, benthic foraminiferal data, and carbon and oxygen isotopes for Eocene hyperthermals: PETM, ETM2, ETM3. Changes in primary productivity, in export of organic carbon from the surface ocean, and in remineralization deeper in the water column in the so-called “twilight zone” may substantially alter the marine biological carbon pump, thus carbon storage in the oceans. We present different proxy records commonly used for reconstructing paleoproductivity, and re-evaluate their use for understanding dynamic change within and between different constituents of the marine biological pump during transient global warming episodes in the past. Marine pelagic barite records are a proxy for carbon export from the photic and/or mesopelagic zone, and are not positively correlated with benthic foraminiferal proxies for arrival of organic matter to the seafloor over three early Eocene periods of global warming (Ocean Drilling Program Site 1263, SE Atlantic). These two proxies reflect processes in different parts of the water column, thus different components of the biological pump.