Sharp peaks in nitrous oxide (N2O) fluxes under no-tillage in wet conditions appear to be related to near surface soil and crop cover conditions. Increasing the downward flux of N2O by changing soil or moisture conditions may increase the chances of its further reduction to N2 or dissolution. We investigated how reducing crop cover by spraying off seedlings in the field and changing the structure of the water filled pore space (WFPS) by short-term laboratory compaction influenced the magnitude and direction of N2O and carbon dioxide (CO2) fluxes. We took undisturbed cores from 3 - 8 cm depth, equilibrated them to -1 or -6 kPa potential, incubated them under non-limiting nitrate conditions and measured N2O and CO2 fluxes from the upper and lower surfaces in a purpose-designed apparatus before and after compaction in an uniaxial tester for 3 minutes. We also measured WFPS, air permeability, bulk density and air-filled porosity before and after laboratory treatment application. Spring barley was tested in 1999 and winter barley in 2000. The effects of laboratory compaction on the fluxes of N2O and CO2 were not influenced greatly by the tillage and crop cover treatments. Fluxes from the upper surfaces of cores (corresponding to 3 cm soil depth) could be up to 4 times greater than from the lower surfaces (8 cm depth). This difference between surfaces was greatest when N2O fluxes were very high in no-tilled soil (4.2 mg N2O-N m-2 h-1) as occurred when the water filled pore system became blocked with water, an effect increased by our compaction treatment. In general N2O fluxes increased with water-filled pore space. Fluxes of N2O were higher from no-tilled than ploughed even where the soil was of similar bulk density possibly due to the greater enzyme activity and organic matter under no-tillage than under ploughing. Nevertheless, the functional capacity of the microbial community to produce N2O was dominated by the soil physical environment produced in no-till vs plough cultivation. Carbon dioxide fluxes differed little between matric potentials and treatments and were not apparently related to any soil physical property. There was no evidence of a relationship between N2O or CO2 flux and soil air-filled porosity or air permeability. Removal of the crop cover increased CO2 flux and could reduce N2O flux. Shallow inversion tillage may influence the direction and magnitude of gas fluxes in no-tilled soil, thereby providing possible mitigation.