Overfishing weakens the ocean’s natural ability to absorb and store carbon dioxide, connecting it to climate change through several biological and physical pathways that researchers have only recently begun to quantify. Fish are not just food or ecological players; they are active participants in the global carbon cycle, moving carbon from surface waters to the deep ocean through their bodies, their waste, and even minerals produced in their guts. By the 1990s, the biomass of commercially exploited fish had been cut nearly in half compared to pre-industrial levels, and that reduction has measurably diminished the ocean’s carbon-processing machinery.
Fish Move Carbon Downward, and Fishing Interrupts That
Before large-scale commercial fishing, the global biomass of exploited fish species weighed roughly 3.3 billion metric tons. These animals collectively cycled about 2% of the ocean’s total primary production and were responsible for around 10% of the biological export of organic matter from the surface to the deep ocean. The waste and dead matter produced by these fish drove roughly a tenth of the oxygen consumption and carbon storage at depth. By the 1990s, both that biomass and its cycling rates had been cut by nearly half, a shift researchers have described as biogeochemically comparable to the effects of anthropogenic climate change itself.1PubMed Central. Estimating global biomass and biogeochemical cycling of marine fish with and without fishing
That statistic deserves emphasis: removing half of the ocean’s fish biomass didn’t just reduce fish populations. It weakened a planetary-scale system for pulling carbon out of the upper ocean and locking it away at depth. The pathways involved are distinct enough to warrant separate attention, because understanding where the carbon goes helps explain why losing fish matters for climate stability.
Dead Fish That Never Reach the Seafloor
Unlike most land animals, whose bodies decompose at the surface and release carbon back into the atmosphere, the carcasses of large marine fish sink when they die. A tuna, a marlin, or a swordfish that dies of natural causes drops through the water column, carrying its carbon into the deep ocean where it can remain locked away for centuries. This process has been called “blue carbon sequestration by deadfall,” and the deep-sea storage time for sinking vertebrate biomass is estimated at around 1,000 years.2PubMed. Industrial fisheries have reversed the carbon sequestration by tuna carcasses into emissions
When fishing vessels catch those same fish before they die naturally, the carbon in their bodies follows a completely different route. It enters the terrestrial food chain, gets processed, and its carbon eventually returns to the atmosphere. Commercial tuna fishing, for instance, not only burns fossil fuel to operate but also eliminates the deadfall of large-bodied fish that would otherwise feed the deep-sea carbon pump.2PubMed. Industrial fisheries have reversed the carbon sequestration by tuna carcasses into emissions One analysis found that much of this lost sequestration occurs in areas where fishing is not even economically profitable, meaning the climate cost comes with questionable economic benefit.3PubMed Central. Let more big fish sink: Fisheries prevent blue carbon sequestration-half in unprofitable areas
The Carbonate Factory Inside Every Bony Fish
Fish contribute to the carbon cycle in a way that has nothing to do with their flesh. Marine bony fish produce calcium carbonate minerals inside their intestines and excrete them continuously throughout their lives. These “ichthyocarbonates” are chemically distinctive: they contain more magnesium than the carbonate produced by plankton or corals, which makes them dissolve faster as they sink through increasingly acidic deeper waters.4PubMed. Contribution of fish to the marine inorganic carbon cycle
Early estimates suggested fish contribute somewhere between 3% and 15% of total oceanic carbonate production.4PubMed. Contribution of fish to the marine inorganic carbon cycle But those estimates were based on older, lower estimates of global fish biomass. When researchers applied updated biomass figures, which suggest the ocean may hold several times more fish than previously thought, the numbers jumped dramatically. Under a median biomass revision, marine fish could be producing between 1.4 and 4.0 billion metric tons of calcium carbonate per year, potentially matching or exceeding the contributions of coccolithophores and foraminifera, the tiny plankton traditionally considered the dominant producers of marine carbonates.5PubMed. Implications of dietary carbon incorporation in fish carbonates for the global carbon cycle
What happens to these carbonates matters for climate. In the North Atlantic, roughly a third of examined ichthyocarbonates sink past 200 meters before dissolving, contributing to deep-water carbon storage. The remaining two-thirds dissolve in shallower water and add alkalinity to the upper ocean, which increases the ocean’s capacity to absorb CO₂ from the atmosphere.6PubMed. The role of marine fish-produced carbonates in the oceanic carbon cycle is determined by size, specific gravity, and dissolution rate Either way, fewer fish means less of this material is being produced, and the ocean’s chemistry is subtly shifted as a result.
When Trawlers Dig Up the Seafloor
Overfishing affects climate not just by removing fish but through the physical methods used to catch them. Bottom trawling, in which heavy nets and gear are dragged across the ocean floor, is one of the most widespread human disturbances to marine sediments. Those sediments are a massive long-term carbon store; organic material that settles on the seafloor and gets buried can remain locked away for millennia. Trawling disrupts that storage by churning up sediment, resuspending organic carbon into the oxygenated water column where microbes can break it down and release CO₂.7Journal of Applied Ecology. Rethinking the impacts of bottom trawling on seabed carbon: Biogeochemical mechanisms, vulnerability and long‐term climate consequences
The result is that areas that functioned as carbon sinks can be transformed into carbon sources. A study of bottom trawling in New Zealand’s Hauraki Gulf used detailed fishing effort data and regional sediment characteristics to estimate CO₂ released from this disturbance, finding that the process turns what should be stable carbon deposits into active emissions.8Ocean & Coastal Management. CO2 release from bottom trawling disturbance and its relevance for seabed management The precise global magnitude remains debated, partly because trawling also reduces the burrowing activity of seafloor organisms and can resuspend nutrients that stimulate new plankton growth, which offsets some of the released carbon.9PubMed Central. The impact of mobile demersal fishing on carbon storage in seabed sediments But the direction of the effect is clear: trawling accelerates carbon release from the seabed.
Coastal Blue Carbon Habitats at Risk
Seagrass beds, saltmarshes, and mangroves are among the most carbon-dense ecosystems on Earth per unit area, and they are collectively known as “blue carbon” habitats. They store carbon in their living biomass and in the sediments beneath them, sometimes accumulating it over centuries. Towed bottom fishing gear poses a direct threat to these habitats. When researchers adapted a risk assessment framework to account for carbon attributes alongside ecological ones, habitats with high organic carbon stocks scored meaningfully higher risk. Seagrass showed the greatest increase in assessed risk, followed by saltmarsh.10PLOS ONE. Adapting the marine stewardship council’s risk-based framework to assess the impact of towed bottom fishing gear on blue carbon habitats
The damage here is twofold. Destroying seagrass or saltmarsh directly releases stored carbon, and it also eliminates the ongoing capacity of those ecosystems to pull more CO₂ out of the water and air. Unlike open-ocean carbon pathways, where the science is still catching up, the carbon value of coastal habitats is well established. Protecting them from destructive fishing practices is one of the more straightforward climate-relevant actions available.
Cascading Effects Through the Food Web
Removing large quantities of fish does not just eliminate the carbon those animals would have processed. It reshapes entire marine food webs in ways that can further weaken carbon sequestration. Small pelagic fish like anchovies, sardines, and herring dominate global catches, and their exploitation can reduce the downward flux of fecal pellet carbon, an important component of the biological pump. It can also trigger trophic cascades that alter plankton communities in unpredictable ways.11PubMed Central. Commercial fishery disturbance of the global ocean biological carbon sink
There is another, less obvious consequence. Many commercially fished species serve as bioturbators, organisms that mix and rework seabed sediments through their feeding and burrowing behavior. On the UK continental shelf alone, 120 out of 185 fish species identified as bioturbators are commercially exploited, and some of the most significant sediment-mixing species are among the most heavily fished.12PubMed. A functional assessment of fish as bioturbators and their vulnerability to local extinction Removing these fish alters the physical and chemical structure of seafloor sediments, with consequences for nutrient cycling and carbon burial that remain poorly understood.
These food web disruptions also affect ecosystem resilience. Research on marine heatwaves has shown that the loss of top predators, whether from fishing or temperature stress, reduces the mean trophic level of fish communities and can destabilize the entire assemblage. Communities dominated by fewer predators and lower trophic levels tend to be less stable, less able to absorb shocks, and less capable of recovering from future disturbances.13PubMed Central. Marine protected areas, marine heatwaves, and the resilience of nearshore fish communities In a warming ocean where extreme events are becoming more frequent, the compounding of overfishing and climate stress makes both problems harder to manage.
What Whaling Taught Us About Marine Carbon
The relationship between overfishing and climate change has a historical parallel in commercial whaling. Before industrial whaling decimated whale populations in the 19th and 20th centuries, great whales played a significant role in marine nutrient cycling. Their feces, released at or near the surface, are rich in iron and nitrogen, nutrients that stimulate phytoplankton growth. More phytoplankton means more photosynthesis, more carbon fixation, and more organic material sinking to depth.
The massive reduction in whale numbers diminished the efficiency of this nutrient recycling in the Southern Ocean, and researchers have argued that recovering whale populations could expand productive regions by returning essential nutrients to surface waters through their waste.14PLOS ONE. The Biogeochemical Role of Baleen Whales and Krill in Southern Ocean Nutrient Cycling Whales also contribute through their own mortality: a whale carcass sinking to the seafloor, known as a “whale fall,” delivers a massive package of carbon to the deep ocean in a single event. Beyond storing and exporting organic carbon, marine animals including fish export inorganic carbon through carbonate excretion, while whales and krill in the Southern Ocean help retain iron in surface waters, fertilizing the base of the food web.15PLOS ONE. The Impact of Whaling on the Ocean Carbon Cycle: Why Bigger Was Better
The whaling story offers a useful lens for understanding overfishing’s climate effects. In both cases, the industrial-scale removal of large marine animals disrupted biological processes that move carbon downward and nutrients upward. The ocean is not just a passive sink; it relies on living organisms to run its carbon cycle, and depleting those organisms degrades the system.
Marine Protected Areas as a Carbon Strategy
If removing fish and disturbing the seabed release carbon, then protecting ocean areas from these activities should, in theory, help preserve or rebuild carbon storage. That logic underpins growing interest in designing marine protected areas with explicit climate goals. One analysis estimated that implementing six ocean-based carbon solutions globally through MPAs, including protecting coastal wetlands, restoring macroalgae, and safeguarding seafloor sediments, could reduce emissions by roughly 16 billion metric tons of CO₂ equivalent by 2060 under a plausible scenario, and around 25 billion metric tons under an ambitious one.16PubMed Central. Climate benefits from establishing marine protected areas targeted at blue carbon solutions
Those numbers amount to roughly 2% of the total carbon mitigation needed to meet Paris Agreement goals for limiting warming to 2°C by 2050. That may sound small, but the blue carbon benefit comes with a package of additional advantages: rebuilding biodiversity, sustaining fisheries in surrounding waters, and protecting coastal communities from storms. Around 70% of the estimated reduction came from active carbon removal, with the remaining 30% from avoided emissions.16PubMed Central. Climate benefits from establishing marine protected areas targeted at blue carbon solutions
Canada has begun explicitly considering seabed sediment carbon in the design of its marine conservation network, recognizing that preventing future releases of stored carbon is a legitimate co-benefit of area-based protection.17FACETS. Protection of seabed sediments in Canada’s marine conservation network for potential climate change mitigation co-benefit This kind of integration is still rare, though. Most MPAs were designed with biodiversity in mind, not carbon, and retrofitting climate objectives onto existing networks requires new data and new management approaches.
Fishing the Twilight Zone
Between roughly 200 and 1,000 meters below the surface sits the mesopelagic zone, sometimes called the ocean’s twilight zone. It is home to an enormous biomass of small fish and other organisms that play a critical role in the carbon cycle through their daily vertical migrations: rising to feed near the surface at night and descending during the day, carrying carbon downward in their bodies and waste. For decades, this zone was considered too deep and too diffuse for commercial fishing to bother with. That assumption has turned out to be wrong.
Recent research drawing on worldwide data and decades of longline catch records has revealed that industrial-scale fishing in the mesopelagic zone has already been happening for years, largely unnoticed by scientists and policymakers. The effects of this exploitation on critical ecosystem services, from regulating the oceanic carbon cycle to sustaining deep food webs, remain unquantified and largely ignored.18Global Change Biology. Hidden in Plain Sight: Decades of Industrial-Scale Fishing in the Ocean’s Twilight Zone This is concerning because the twilight zone is thought to be responsible for a substantial share of the biological carbon pump’s total output. Fishing it without understanding the consequences could undermine one of the ocean’s most important and least visible climate services.
Why Fish Are Missing from Climate Models
Given all of these pathways, you might expect fish to feature prominently in global climate models and carbon accounting frameworks. They do not. The role of fish in the carbon cycle is still poorly integrated into the models that inform climate policy. Fishing has modified the distribution and abundance of fish worldwide and consequently may have altered the nutrient cycling that fish mediate, but this possibility remains largely unassessed, mainly because estimating global fish biomass and metabolic rates is extremely difficult.19Biogeosciences. Global nutrient cycling by commercially targeted marine fish
The uncertainties in fish carbonate composition and production rates have so far prevented researchers from plugging fish into fully coupled carbon-climate models.5PubMed. Implications of dietary carbon incorporation in fish carbonates for the global carbon cycle Realizing the carbon benefits of ocean-based solutions more broadly is constrained by monitoring, reporting, and verification costs, data gaps, and methodological challenges that make it hard to turn marine carbon science into usable policy tools.20Annual Review of Environment and Resources. Blue Carbon in an Era of Carbon Accounting
This gap has real consequences. If the carbon cost of overfishing is invisible in the accounting systems that guide international policy, then fisheries management remains disconnected from climate goals. A trawler that destroys a seabed carbon store or a fleet that halves a tuna population does not currently bear any carbon liability for doing so. Until fish carbon is measured well enough to count, it will continue to be treated as though it does not exist, even as the evidence mounts that it very much does.