Methane and nitrous oxide have separated production zones and distinct emission pathways in freshwater aquaculture ponds.

Aquaculture systems receive intensive carbon (C) and nitrogen (N) loadings, and are therefore recognized as major anthropogenic sources of methane (CH) and nitrous oxide (NO) emissions. However, the extensively managed aquaculture ponds were identified as a hotspot of CH emission but just a weak NO source. Here, we investigate annual CH and NO fluxes from three earthen ponds used for crab culture, of different sizes, in southeast China. Our purposes are to identify the spatiotemporal variations of CH and NO emissions and their components among ponds and to evaluate the zone for CH and NO production. Static chamber-measured CH flux ranged from 0.03 to 64.7 mg CH m h (average: 9.02‒14.3 mg CH m h), and temperature, followed by dissolved organic C (DOC) concentration, and redox potential, were the primary drivers of seasonal CH flux patterns. Annual mean diffusive CH flux was 1.80‒2.34 mg CH m h, and that by ebullition was up to 7.20‒12.0 mg CH m h (79.1‒83.5% of the total CH flux). Annual CH emission was positively correlated with sediment DOC concentration but negatively (P < 0.05) correlated with water depth across ponds, with the highest CH emission occurred in a pond with low water depth and high DOC concentration. The calculated diffusive NO flux by the gas transfer velocity was 0.32‒0.60 times greater than the measured NO emission, suggesting that NO in water column can not only evade as water-air fluxes but diffuse downwards and to be consumed in anaerobic sediments. This also indicates that NO was primarily produced in water column. The highly reduced condition and depletion of NO-N in sediments, can limit NO production from both nitrification and denitrification but favor NO consumption, leading the ponds to become a weak source of NO annually and even a sink of NO in summer. Our results highlight that the current global CH budget for inland waters is probably underestimated due to a lack of data and underestimation of the contribution of ebullitive CH flux in small lentic waters. The downwards NO diffusion from the water column into sediment also indicates that the extensively-used model approach based on gas transfer velocity potentially overestimates NO fluxes, especially in small eutrophic aquatic ecosystems.