The influence of different depths of repacked soil cores on changes in N transformation processes was studied with a subtropical semi-arid soil amended with 100 mg N kg-1 of Sesbania green manure (GM) or fertilizer (NH4)2SO4 for 35 days under flooded and nonflooded conditions. Shallow soil depth enhanced the rate of nitrification, particularly where aeration was impeded in flooded soils. However, the opposite occurred for denitrification as the relative predominance of underlying anoxic zone increased with increase in soil depth. Nitrate produced in the thin oxic surface soil layer and overlying water in flooded soils was subsequently lost via denitrification, more rapidly where carbon was supplied by added GM. Decomposition of GM was rapid and apparent recovery of applied 100 mg GM-N kg-1 soil as mineral N after 35 days in flooded soils was 8, 26, 30 and 38% in 1.25-, 2.5-, 5.0- and 7.5-cm deep soil cores, respectively. Soil ammonium-N declined rapidly after an initial rise during decomposition of GM in soil in the shallow soil depth. In contrast, no such decline in NH 4 + -N was observed in deep soil cores. In conclusion, the use of shallow soil depths during laboratory incubations can lead to variable results under flooded conditions. To simulate field conditions for obtaining reliable and quantitative information regarding N transformations in soils under flooded conditions, soil depths of 7.5 cm or greater should be used for laboratory incubations and growth chamber studies.