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Abstract An experiment was conducted to investigate the effect of precipitation and N deposition on N 2 O and CH 4 fluxes and soil respiration (R s) in the Gurbantunggut Desert from September 2014 to August 2015. The desert was a weak sink for CH 4 (−0.92 kg C ha−1 yr−1) and a small source of N 2 O (+0.13 kg N ha−1 yr−1) and the annual rate of R s was 874 kg C ha−1. Our work confirmed a relatively strong sink for CH 4 in desert soils. Significant impacts on N 2 O, CH 4 fluxes and R s were found by increasing precipitation, with pulses of CH 4 uptake and R s accounting for 79.1% and 33.2% of annual CH 4 uptake and R s , respectively. N 2 O and CH 4 fluxes were significantly enhanced by 7.8–109.6% by N addition, but it had no significant effect on R s. Statistical significant interactions of precipitation and N addition on N 2 O and CH 4 fluxes were found, and on R s was lower than any single factor. Our results indicate that the Gurbantunggut Desert is a weak sink for CH 4 and a small source of N 2 O, and is sensitive to elevated precipitation and N deposition. Highlights • The Gurbantunggut Desert was a weak sink for CH 4 and source of N 2 O. • N 2 O and CH 4 fluxes were significantly increased by precipitation and N deposition. • Significant interactive effects of water and N on N 2 O and CH 4 fluxes were found. • Interactive effects of water and N on soil respiration were lower than any single factor. [ABSTRACT FROM AUTHOR]