Aquaculture plays a crucial role in meeting the increasing demand for protein-rich food. However, aquaculture production also comes with a large carbon footprint, partly due to the substantial emission of greenhouse gases, particularly methane (CH₄), during the aquaculture production. Yet, our understanding on the magnitude, pathways, and drivers of CH4 emission from aquaculture ponds is limited, particularly in the Asian continent where more than 90% of global aquaculture production occurs. In this study, we quantified CH4 concentrations, air–water fluxes, production in anoxic sediments, and oxidation in the water column across multiple tropical aquaculture ponds where one of the most commonly cultivated shrimp species, Litopenaeus vannamei, is farmed. Field measurements showed that the diffusive CH4 emissions, with a mean value of 3.40 ± 1.76 mg m−2 day−1, varied greatly—ranging from 0.68 to 7.12 mg m−2 day−1—and were regulated by a suit of environmental variables. Salinity and total phosphorus (TP) concentration were the key determinants of diffusive CH4 flux: CH4 emission decreased with increasing salinity, while it increased with TP. Accordingly, our results suggest that shifting from freshwater to saline water aquaculture can decrease CH₄ emissions, thereby reducing the carbon footprint of aquaculture production. However, an increase in phosphorus concentration can offset this salinity-driven emission reduction. Therefore, management practices should prioritize reducing phosphorus loads to effectively mitigate CH₄ emissions and enhance the sustainability of aquaculture. © The Author(s), under exclusive licence to Springer Nature Switzerland AG 2025.
