Micrometeorological methods are ideally suited for continuous measurements of N₂O fluxes, but gaps in the time series occur due to low-turbulence conditions, power failures, and adverse weather conditions. Two gap-filling methods including linear interpolation and artificial neural networks (ANN) were utilized to reconstruct missing N₂O flux data from a corn–soybean–wheat rotation and evaluate the impact on annual N₂O emissions from 2001 to 2006 at the Elora Research Station, ON, Canada. The single-year ANN method is recommended because this method captured flux variability better than the linear interpolation method (average R² of 0.41 vs. 0.34). Annual N₂O emission and annual bias resulting from linear and single-year ANN were compatible with each other when there were few and short gaps (i.e., percentage of missing values <30%). However, with longer gaps (>20 d), the bias error in annual fluxes varied between 0.082 and 0.344 kg N₂O-N ha^-1 for linear and 0.069 and 0.109 kg N₂O-N ha^-1 for single-year ANN. Hence, the single-year ANN with lower annual bias and stable approach over various years is recommended, if the appropriate driving inputs (i.e., soil temperature, soil water content, precipitation, N mineral content, and snow depth) needed for the ANN model are available.