The late Paleocene to the early Eocene (∼58–52 Ma) was marked by significant changes in global climate and carbon cycling. The evidence for these changes includes stable isotope records that reveal prominent decreases in δ18O and δ13C, suggesting a rise in Earth's surface temperature (∼4°C) and a drop in net carbon output from the ocean and atmosphere. Concurrently, deep-sea carbonate records at several sites indicate a deepening of the calcite compensation depth (CCD). Here we investigate possible causes (e.g., increased volcanic degassing or decreased net organic burial) for these observations, but from a new perspective. The basic model employed is a modified version of GEOCARB III. However, we have coupled this well-known geochemical model to LOSCAR (Long-term Ocean-atmosphere Sediment CArbon cycle Reservoir model), which enables simulation of seawater carbonate chemistry, the CCD, and ocean δ13C. We have also added a capacitor, in this case represented by gas hydrates, that can store and release13C-depleted carbon to and from the shallow geosphere over millions of years. We further consider accurate input data (e.g., δ13C of carbonate) on a currently accepted timescale that spans an interval much longer than the perturbation. Several different scenarios are investigated with the goal of consistency amongst inferred changes in temperature, the CCD, and surface ocean and deep ocean δ13C. The results strongly suggest that a decrease in net organic carbon burial drove carbon cycle changes during the late Paleocene and early Eocene, although an increase in volcanic activity might have contributed. Importantly, a drop in net organic carbon burial may represent increased oxidation of previously deposited organic carbon, such as stored in peat or gas hydrates. The model successfully recreates trends in Earth surface warming, as inferred from δ18O records, the CCD, and δ13C. At the moment, however, our coupled modeling effort cannot reproduce the magnitude of change in all these records collectively. Similar problems have arisen in simulations of short-term hyperthermal events during the early Paleogene (Paleocene-Eocene Thermal Maximum), suggesting one or more basic issues with data interpretation or geochemical modeling remain.