We studied the effects of water regimes and nutrient amendments on CH4 and N2O emissions in a 2 × 3 factorial, completely randomised growth chamber experiment. Treatments included continuously flooded (CF) and alternate wetting and drying (AWD), and three organic amendments: no amendment-control, rice straw (RS) and biochar (BC). Compound fertiliser was applied to all treatments. Rice was grown in columns packed with a paddy soil from Cambodia. Results revealed faster mineralisation of organic carbon (RS and BC) when applied in water-saturated conditions lasting for 2 weeks instead of flooding. This resulted in lower total CH4 emissions in treatments under AWD than those under the CF water regime, namely 44 % in RS treatments and 29 % in BC treatments. Nitrous oxide fluxes were generally non-detectable during the experimental period except after fertilisation events, and the total N2O–N emissions accounted for on average 1.7 % of the total applied mineral fertiliser N. Overall, the global warming potentials (GWPs) were lower in treatments under AWD than those under the CF water regime except for the control treatment with only mineral fertiliser application. Grain yields were slightly higher in treatments under AWD than the CF water regime. Hence, the yield-scaled GWP was also lower in the treatments under the AWD water regime, namely 51 % in RS, 59 % in BC and 17 % in control treatments. Control treatments had the lowest GWP, but provided the highest yield. The yield-scaled GWP under these treatments was therefore lower than under the other treatments.