Today, the key role played by oceans in the Earth's carbon cycle is widely recognized. The important boundary to consider is not the ocean-atmosphere interface, across which the carbon dioxide (CO₂) concentration gradient is small, but the seasonal and permanent thermoclines, whose positions range from about 20 to 300 meters in depth. Once CO₂ is delivered to depths beyond these thermoclines, the sequestration efficiency for CO₂ is increased.

Both physical and biological pumps act to increase the amount of carbon stored in the deep sea. For the latter process, more than 90% of the organic carbon exported (10–12 gigatons per year) to the deeper mesopelagic waters (i.e., the region below the upper mixed layer down to about 1000 meters, also called the twilight zone) is again respired to form CO₂. Only a very small fraction of this organic carbon (<1%) eventually reaches the seafloor, where it is sequestered on longer timescales. The mechanisms controlling carbon export and its fate are still insufficiently understood to allow an informed assessment of its variability.