Methane (CH4), the second largest non-vapor greenhouse gas, has larger global warming threat than carbon dioxide (CO2). Atmospheric CH4 levels have spiked since the industrial revolution, with rivers identified as significant CH4 contributors. However, understanding the sources and dynamics of dissolved CH4 in rivers remains a challenge. Our study focuses on the Pearl River Basin (PRB) in China, examining CH4 dynamics across two distinct hydrologic seasons. Dissolved CH4 concentrations in the PRB varied widely, from 4 to 15126 nM, with higher levels during the wet season (681 ± 1508 nM) compared to the dry season (349 ± 328 nM). At the basin scale, dissolved CH4 was under the co-control of thermogenic source as background input (35 %) and biogenic source as the high-concentration source (65 %). The Pearl River network is a CH4 source and annually, 25.96 ± 32.6 Gg C of CH4 evades into the atmosphere via diffusion. The total CH4 emissions (diffusion + ebullition) account to more than 50 % warming potential of CO2 emission from the PRB. Without considering CH4 consumption by oxidation at the sediment–water interface and river water column, the hyporheic zone contributes 286 % and 414 % of CH4 emission to the atmosphere in the dry and wet seasons, respectively. The hyporheic zone is a “hotspot” for biogenic CH4 production, but our results underlines that the hyporheic zone may also be a conduit medium for the transportation of groundwater derived CH4 into rivers. Furthermore, dissolved CH4 evades from the hyporheic zone into river channels at greater rates in larger rivers. These findings underscore the critical role of rivers in atmospheric CH4 levels and highlight the need for a deeper understanding of CH4 dynamics in the hyporheic zone. This knowledge is essential to complete the regional and global carbon cycle puzzle and address the urgent environmental challenges posed by greenhouse gases.
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