The transformation, via photosynthesis in the ocean surface layer by plant cells (primarily phytoplankton), of dissolved inorganic carbon (DIC) into biogenic carbon, including, for example, the CaCO³ in shells of coccolithophorids. The photosynthetic organisms incorporating the inorganic carbon return much of it to CO² in the surface layer via respiration, but a significant fraction settles below the main thermocline. This is an oceanic sink for atmospheric CO² where a rain of small debris consisting of phytoplankton shells and zooplankton fecal pellets and molts sink out of the ocean surface waters. These sinking particles remove POC from surface mixed layers into stratified, relatively deep layers where, on a millenial time scale, it is no longer susceptible to exchange with the atmosphere. Particulate matter removed in this manner is called export flux.

It is estimated that 75% of the difference in DIC concentration between the surface and deep oceans is due to the biological pump. If this pump were eliminated, the carbon released from the deep ocean as it equilibrated with the atmosphere would more than double the CO2 concentration in the atmosphere. On a global scale, the downward transport of CO² by the physical (i.e. vertical transport of CO²-laden water) and biological pumps amounts to around 102 Gt C yr^-1. The upward physical transport is about 100 Gt C yr^-1, leaving a net uptake of about 2 Gt C yr^-1.