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Fisheries capture has plateaued, creating ever-greater reliance on aquaculture to feed growing populations. Aquaculture volumes now exceed those of capture fisheries globally(1,2), with China dominating production through major land-use change; more than half of Chinese freshwater aquaculture systems have been converted from paddy fields(1,3). However, the greenhouse gas implications of this expansion have yet to be effectively quantified. Here, we measure year-round methane (CH4), nitrous oxide (N2O) and carbon dioxide (CO2) emissions from paddy fields and new, extensively managed crab aquaculture ponds. The conversion increased associated global warming potentials from 8.15 +/- 0.43 to 28.0 +/- 4.1 MgCO(2)eq ha(-1), primarily due to increased CH4 emissions. After compiling a worldwide database of different freshwater aquaculture systems, the top 21 producers were estimated to release 6.04 +/- 1.17 TgCH(4) and 36.7 +/- 6.1 GgN(2)O in 2014. We found that 80.3% of the total CH4 emitted originated in shallow earthen aquaculture systems, with far lower emissions from intensified systems with continuous aeration(4). We therefore propose that greater adoption of aerated systems is urgently required to address globally significant rises in CH4 emissions from the conversion of paddy fields to aquaculture.