Sea surface and subsurface temperatures over large parts of the ocean during the Eocene epoch (55.5-33.7 Ma) exceeded modern values by several degrees, which must have affected a number of oceanic processes. Here, we focus on the effect of elevated water column temperatures on the efficiency of the biological pump, particularly in relation to carbon and nutrient cycling. We use stable isotope values from exceptionally well-preserved planktonic foraminiferal calcite from Tanzania and Mexico to reconstruct vertical carbon isotope gradients in the upper water column, exploiting the fact that individual species lived and calcified at different depths. The oxygen isotope ratios of different species' tests are used to estimate the temperature of calcification, which we converted to absolute depths using Eocene temperature profiles generated by general circulation models. This approach, along with potential pitfalls, is illustrated using data from modern core-top assemblages from the same area. Our results indicate that, during the Early and Middle Eocene, carbon isotope gradients were steeper (and larger) through the upper thermocline than in the modern ocean. This is consistent with a shallower average depth of organic matter remineralization and supports previously proposed hypotheses that invoke high metabolic rates in a warm Eocene ocean, leading to more efficient recycling of organic matter and reduced burial rates of organic carbon.