Little work has been done on nitrous oxide (N2O) emissions from nitrogen-fertigation systems, despite the greater degrees of control allowed over fertilizer N fate. More fertigation users are adopting high-frequency (HF) N application schedules to improve nitrogen use efficiency and reduce nitrate (NO3−) leaching. The possibility is raised that this practice may also lower N2O emissions, through effects on soil N concentrations and soil microbial populations. At the same time, NO3-based N-fertilizers are frequently selected for use in HF systems, where they should be more immediately available to plants than ammoniacal fertilizers. This choice of N-source is likely to affect N2O emissions. We monitored surface emissions of N2O in an almond orchard (Prunus dulcis [Mill.] DA Webb) in Belridge, California. Fertigation treatments were 4xyear−1 (Standard) urea ammonium nitrate (UAN), 20xyear−1 (HF) UAN and 20xyear−1 (HF) CaNO3+KNO3. Estimated surface emissions were HF UAN>Standard UAN>HF NO3, with differences only significant between the HF treatments, where HF UAN emitted 2.0 times the N2O seen from HF NO3. Net production was also monitored by depth in the soil using sampling tubes and Fickian diffusion calculations. UAN typically had highest N2O production at 10–15cm depth, while N2O was generally reduced to N2 below 20cm in all treatments. Differences were seen in the distribution of NH4+ and NO3− on the soil exchange complex and in soil solution, with data from 60cm suggesting that leaching hazards could be greater from Standard UAN than from HF NO3. Multiple linear regression of N2O production with predictors had the best fit at 15cm, where extractable NH4+, WFPS and temperature together accounted for an adjusted R2 of 0.68. Persistent soil microbial changes were seen in denitrification capacity, with HF UAN=HF NO3>Standard UAN, while 3% O2 assays suggested high contributions of N2O from nitrifier denitrification in the fertigation context. High-frequency fertigation with ammoniacal fertilizers did not mitigate N2O emissions, but nitrate-based fertilizers did, suggesting that N sources for fertigation warrant careful study.