Just like the solubility pump, the biological pump also cycles carbon through the ocean. This process involves plants, animals, and bacteria.

Like in forests, plants in the ocean photosynthesize. We find most of the oceans plants, which are called phytoplankton, in the uppermost layer of the ocean where there is plenty of light. To photosynthesize, the plankton needs the CO₂ that is dissolved in the water. Once the plankton has taken up CO₂ for photosynthesis, it makes new cells from that carbon, grows and reproduces, and creates a new generation of plankton.

Tiny animals called zooplankton eat the phytoplankton. The zooplankton, in turn exhale and ingest carbon as CO₂, returning to the water some of the gas that was taken up by the plankton.

However, not all of the plankton is eaten, and under certain conditions, it clumps together with other plankton and particles, making an aggregate heavy enough to sink. As fecal pellets and dead plankton sink, animals and bacteria in the deep ocean eat the particles raining from above. In turn, they get their growth and reproductive energy from the food and respire the carbon back to CO₂.

So, through this process called the biological pump, carbon is moved from the upper layer of the ocean to the deep sea—there, joining the already high CO₂ introduced elsewhere by the solubility pump. Together, those vast amounts of gas are returned to the atmosphere at the upwelling sites.