The ocean has long served as one of the planet’s most vital buffers against climate change, absorbing both excess heat and a large share of carbon dioxide emitted by human activity. Yet new research warns that marine heat waves are undermining one of the ocean’s most important natural functions—the ability to flush carbon from the surface into the deep sea.

This vast “carbon toilet,” as some scientists describe it, operates through the smallest of ocean inhabitants. Microscopic plants known as phytoplankton absorb carbon dioxide through photosynthesis, forming the foundation of the marine food chain. Tiny animals called zooplankton feed on them and release carbon-rich fecal pellets that normally sink to the seafloor. This downward flow effectively locks carbon away for centuries, helping to regulate Earth’s climate.

But recent prolonged heat waves in the northeastern Pacific Ocean have disrupted this mechanism. Long-term data from autonomous ocean-monitoring floats show that unusually warm waters between 2013 and 2020 changed the composition and behavior of plankton communities, reducing the amount of carbon that sinks into the depths.

During these events, ocean temperatures surged due to atmospheric warming and a lack of wind-driven mixing that typically brings cooler, nutrient-rich water to the surface. As a result, the upper layer of the sea became warmer, less dense, and more stagnant, forming a cap that trapped heat near the surface. Without the usual winter churning, nutrients from deeper waters failed to reach phytoplankton living in the sunlit zone.

Deprived of key nutrients, larger species of phytoplankton—normally efficient at capturing carbon and supporting the food web—declined. In their place, smaller species that require fewer nutrients began to dominate. This shift cascaded through the food chain. Smaller phytoplankton attracted smaller zooplankton, which produced much finer fecal pellets. Instead of sinking rapidly to the seafloor, these tiny particles tended to remain suspended in midwater, where they were further broken down by other organisms.

Measurements taken throughout the water column revealed that during both heat waves, carbon particles were accumulating at depths between 200 and 400 meters rather than descending to the deep ocean. Grazers feeding at these depths fragmented the material even more, preventing it from sinking. In the second heat wave, which coincided with a decline in ocean salinity and a stronger surface cap, the proportion of small zooplankton increased, worsening the blockage.

As this “carbon toilet” became clogged, more organic matter accumulated near the surface, where bacteria decomposed it, releasing carbon dioxide back into the surrounding water. Over time, ocean currents are expected to return this carbon-rich water to the surface, allowing the gas to escape into the atmosphere—reversing the very process that keeps global temperatures in check.

The findings highlight a growing concern about how marine heat waves could weaken the ocean’s role as a carbon sink. Currently, the seas absorb about a quarter of humanity’s annual carbon emissions. If prolonged warming continues to impair this biological pump, more carbon could remain in the atmosphere, accelerating climate change.

Marine heat waves are becoming more intense and widespread as the planet warms. In the 19th century, only about 2 percent of the ocean surface experienced such events. Today, that figure exceeds 50 percent, and the frequency is expected to rise sharply unless emissions are drastically reduced. The northern Pacific, already reeling from two record-setting warm spells, is once again registering unusually high temperatures.

The implications go beyond climate regulation. Disruptions at the base of the food web threaten the entire marine ecosystem. Phytoplankton produce much of the oxygen humans breathe and form the primary food source for countless ocean species, from tiny crustaceans to massive whales. Reduced productivity at this level could reverberate through the food chain, altering biodiversity and fisheries alike.

With thousands of automated Biogeochemical Argo floats now monitoring oceans worldwide, researchers are beginning to piece together how these dynamics unfold in different regions. The emerging picture is sobering: as oceans heat and stratify, their capacity to absorb and store carbon diminishes, transforming one of the planet’s greatest climate allies into a less reliable buffer.

The study serves as a stark reminder that warming seas are not just a symptom of climate change—they are also shaping its future trajectory. If marine heat waves continue to interfere with the ocean’s carbon cycle, the world’s largest carbon sink may no longer be able to flush away humanity’s growing emissions, leaving more heat-trapping gas in the sky and less hope for a stable climate.