<p>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, <i>Litopenaeus vannamei</i>, is farmed. Field measurements showed that the diffusive CH₄ emissions, with a mean value of 3.40 ± 1.76&#xa0;mg&#xa0;m⁻²&#xa0;day⁻¹, varied greatly—ranging from 0.68 to 7.12&#xa0;mg&#xa0;m⁻²&#xa0;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.</p>