Fisheries capture has plateaued, creating ever-greater reliance on aquaculture to feed growing populations. Aquaculture volumes now exceed those of capture fisheries globally1,2, with China dominating production through major land-use change; more than half of Chinese freshwater aquaculture systems having been converted from paddy fields1,3. However, the greenhouse gas (GHG) 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 (GWP) from 8.15 ± 0.43 to 28.0 ± 4.1 Mg CO2 eq ha–1, primarily due to increased CH4 emission. After compiling a worldwide database of different freshwater aquaculture systems, the top 21 producers were estimated to release 6.04 ± 1.17 Tg CH4 and 36.7 ± 6.1 Gg N2O in 2014. We found that 80.3% of total CH4 emitted originated in shallow earthen aquaculture systems, with far lower emissions from intensified systems with continuous aeration4. We therefore propose greater adoption of aerated systems is urgently required to address globally significant rises in CH4 emission from the conversion of paddy fields to aquaculture.