We measured nitrous oxide (N2O) emission from the infralittoral zone and pelagic zone in a shallow lake on the Tibetan Plateau during the growing season of 2009, prior to the lake restoration project aiming to raise the lake water by 0.5–1 m. Mean flux rates of N2O were 0.054 ± 0.094 mg N2O m−2 h−1 and 0.009 ± 0.072 mg N2O m−2 h−1 from infralittoral zone and pelagic zone respectively. Submerged plant biomass index (SPBI) (R = 0.43, P < 0.01, n = 16), nitrate content in surface sediment (R = 0.22, P < 0.05, n = 16) and surface sediment temperature (R = 0.79, P = 0.000, n = 16) were found to significantly correlated to the spatial pattern of N2O flux. Nitrates loading gradient across (sub) zones along with the enhancing effect of plant on nitrate removal were thought to be responsible for this spatial pattern of N2O flux, while temperature act as a regulator on denitrification. Infralittoral zone had the greatest relative contribution (62.2%) of N2O emission to the whole lake budget among various (sub) zones, indicating infralittoral zone a vital component of N2O emission from shallow lakes. As the consequence of the lake restoration project, the response of N2O flux to the raised water depth might vary from different (sub) zones, therefore further study should be conducted so as to have a better understanding on the effect of restoration project on the overall N2O flux from the lake.