Fish raise lake carbon dioxide levels through several overlapping mechanisms, from the simple act of breathing to more complex effects on food webs and lake sediments. While any single fish contributes a tiny amount, the combined impact of an entire fish population can meaningfully shift a lake’s carbon balance.
Respiration Through the Gills
The most direct way fish add CO2 to lake water is by breathing. Like all animals, fish burn food for energy through cellular respiration, producing carbon dioxide as a waste product. That CO2 travels through the bloodstream as bicarbonate, enters red blood cells, and is converted back into dissolved CO2 before diffusing out across the thin tissue of the gills and into the surrounding water.
The rate of CO2 output scales with body size and activity level. Measurements from the U.S. Bureau of Reclamation found that a small freshwater species, the threadfin shad, produces roughly 0.7 milligrams of CO2 per gram of body weight per hour. That may sound negligible for a single fish, but a lake holding thousands of kilograms of total fish biomass generates a continuous, substantial stream of dissolved CO2 around the clock. Warmer water temperatures and higher activity levels push these rates even higher.
Trophic Cascades and Phytoplankton Blooms
Fish also increase lake CO2 indirectly by reshaping the food web. Many common lake fish feed heavily on zooplankton, the tiny animals that graze on algae and other phytoplankton. When fish reduce zooplankton populations, or shift them toward smaller, less effective grazers, phytoplankton escape their main source of population control. Experiments published in PLOS One showed that enclosures stocked with planktivorous fish lost effective grazing pressure on phytoplankton entirely, even after the fish were removed. The zooplankton community shifted to smaller species that couldn’t suppress algae growth, regardless of how numerous they became.
This matters for CO2 because of what happens after a bloom. While actively growing, phytoplankton pull CO2 from the water through photosynthesis. But uncontrolled blooms eventually crash. The dead algae sink and decompose, and the bacteria breaking them down consume oxygen and release large pulses of CO2 back into the water. In lakes with heavy fish predation on zooplankton, this boom-and-bust cycle repeats more intensely, generating more decomposition-driven CO2 than a lake where zooplankton keep algae in check year-round.
Stirring Up the Bottom
Bottom-feeding fish like carp physically churn lake sediments while foraging, a process called bioturbation. This has a surprisingly strong effect on greenhouse gas emissions. Mesocosm experiments using common carp found that their digging introduces oxygen into sediment layers that would otherwise remain oxygen-poor. That extra oxygen fuels aerobic decomposition of organic material buried in the mud, which releases CO2.
There’s an interesting tradeoff here. Oxygen-poor sediments normally produce methane, a far more potent greenhouse gas. When carp stir things up, methane emissions drop because the added oxygen allows bacteria to break down organic matter through a different chemical pathway. But the increase in CO2 emissions more than offsets the methane reduction, resulting in higher total greenhouse gas output from the lake overall. In lakes with large populations of bottom feeders, this sediment disturbance can be a major and often overlooked source of carbon dioxide.
Fish Waste and Carbonate Excretion
Beyond respiration, fish release carbon through their digestive waste. Research published in Science revealed that fish produce calcium carbonate crystals inside their intestines and excrete them continuously. While the study focused on marine fish (estimating they contribute 3 to 15% of total oceanic carbonate production), freshwater fish use similar digestive chemistry. These carbonates dissolve at varying rates depending on water conditions, and their breakdown ultimately contributes to the pool of dissolved inorganic carbon in the water column.
Fish feces and uneaten food also settle on the lake bottom, adding to the organic sediment that bacteria decompose into CO2. Nutrient-rich waste, particularly ammonia and phosphorus compounds, can further fertilize algal growth, feeding back into the bloom-crash-decomposition cycle described above.
Why Fish Density Matters
All of these effects intensify as fish populations grow. Aquaculture research has documented that high fish densities in enclosed systems cause metabolic waste products, including CO2 and ammonia, to accumulate rapidly when water circulation is limited. Natural lakes aren’t as confined as fish farms, but the same principle applies at scale. Overstocked lakes, whether from fish introductions, loss of predators, or nutrient pollution fueling prey abundance, experience amplified versions of every mechanism listed above: more respiration, more zooplankton suppression, more sediment disturbance, and more organic waste.
Shallow, warm, nutrient-rich lakes are especially vulnerable. These conditions support dense fish populations, accelerate metabolic rates, and promote the kind of intense algal cycling that generates repeated CO2 pulses. In many such lakes, the biological activity driven by fish is a significant reason the water remains supersaturated with CO2 relative to the atmosphere, meaning the lake acts as a net source of carbon dioxide rather than a sink.