A 3-year field experiment was conducted to simultaneously measure methane (CH4) and nitrous oxide (N2O) emissions from rice paddies under various agricultural managements including water regime, crop residue incorporation, and synthetic fertilizer application. In contrast with continuous flooding, midseason drainage incurred a drop in CH4 fluxes while triggering substantial N2O emission. Moreover, N2O emissions after midseason drainage depended strongly on whether or not fields were waterlogged due to intermittent irrigation. Urea application tended to reduce CH4 emissions but significantly increased N2O emissions. Under a water regime of flooding-midseason drainage-reflooding-moist intermittent irrigation but without water logging (F-D-F-M), both wheat straw and rapeseed cake incorporation increased CH4 emissions by 252%, and rapeseed cake increased N2O by 17% while wheat straw reduced N2O by 19% compared to controls. Seasonal average fluxes of CH4 ranged from 25.4 mg m−2 d−1 when no additional residue was applied under the water regime of flooding-midseason drainage-reflooding to 116.9 mg m−2 d−1 when wheat straw was applied at 2.25 t ha−1 under continuous irrigation flooding. Seasonal average fluxes of N2O varied between 0.03 mg N2O-N m−2 d−1 under continuous flooding and 5.23 mg N2O-N m−2 d−1 under the water regime of F-D-F-M. Both crop residue-induced CH4, ranging from 9 to 15% of the incorporated residue C, and N2O, ranging from 0.01 to 1.78% of the applied N, were dependent on water regime in rice paddies. Estimations of net global warming potentials (GWPs) indicate that water management by flooding with midseason drainage and frequent water logging without the use of organic amendments is an effective option for mitigating the combined climatic impacts from CH4 and N2O in paddy rice production.