The aim of this study was to evaluate the pattern of nitrous oxide (N 2O) and methane (CH 4) fluxes, and leaching losses of nitrate (NO 3-) and dissolved organic C (DOC), during a fallow-onion crop-fallow cycle in a Mediterranean area. The importance of the fallow (intercrop) period and the type of fertilizer were also evaluated. Goat and chicken manure (M) from an organic farm, digested pig slurry (DPS) and urea (U) were applied at a rate of 110 kg N ha -1 and compared with a zero N treatment (Control). The crop period contributed more than each fallow period to the total N 2O emission (ranging from 70 to 85% of the total emission, depending on the treatment). The variability of rainfall during fallow periods affected N 2O emissions, with the highest fluxes observed in the second fallow, which was the wetter. Negative net fluxes of N 2O (0 to -0.4 mg N 2O-N m -2 day -1) were mainly observed during the irrigation period and in fallow periods. The type of fertilizer had no effect on N 2O fluxes, but influenced the CH 4 oxidation. The largest CH 4 emission was from the manure treatment (2.4 mg CH 4-C m -2 day -1) during the irrigation period. The lowest NO 3- but highest DOC leaching rates were measured during the second fallow period from the manure treated plots (0.2 kg NO 3--N ha -1 and 3.9 kg C ha -1), which also had the highest drainage. The use of OM, therefore, seems to be a suitable method to reduce the environmental impacts associated with N leaching as well as increase the potential to denitrify NO 3- in groundwater.