During the Eocene-Oligocene transition (EOT, ca. 34 Ma), Earth's climate cooled significantly from a greenhouse to an icehouse climate, while the calcite (CaCO3) compensation depth (CCD) in the Pacific Ocean increased rapidly. Fluctuations in the CCD could result from various processes that create an imbalance between calcium (Ca) sources to, and sinks from, the ocean (e.g., weathering and CaCO3 deposition), with different effects on the isotopic composition of dissolved Ca in the oceans due to differences in the Ca isotopic composition of various inputs and outputs. We used Ca isotope ratios (δ44/40Ca) of coeval pelagic marine barite and bulk carbonate to evaluate changes in the marine Ca cycle across the EOT. We show that the permanent deepening of the CCD was not accompanied by a pronounced change in seawater δ44/40Ca, whereas time intervals in the Neogene with smaller carbonate depositional changes are characterized by seawater δ44/40Ca shifts. This suggests that the response of seawater δ44/40Ca to changes in weathering fluxes and to imbalances in the oceanic alkalinity budget depends on the chemical composition of seawater. A minor and transient fluctuation in the Ca isotope ratio of bulk carbonate may reflect a change in isotopic fractionation associated with CaCO3 precipitation from seawater due to a combination of factors, including changes in temperature and/or in the assemblages of calcifying organisms.