Methane and nitrous oxide are potent greenhouse gases. Even small fluxes of these gases from blue carbon ecosystems can significantly offset the uptake of carbon dioxide, which results in the formation of sequestered organic matter.

The production and consumption of methane and nitrous oxide are regulated by microbial activities and are influenced by a number of environmental factors, including water level, electron acceptor availability, organic matter, and plants.

Measurement of methane and nitrous oxide fluxes can be accomplished by laboratory incubations, modeling and direct field measurements using chambers or eddy covariance approaches. These measurements vary in complexity and appropriateness for defining greenhouse gas fluxes from ecosystems.