Extensive in situ monitoring in a young commercial apple orchard demonstrated that current management practices resulted in leaching of 56 to 84 kg ha1 yr1 of nitrate below the topsoil. The Hydrus 2D/3D suite of models was used to determine the effect of current management practices on nitrate leaching and explore options for reducing irrigation and nitrate loss. The models were parameterized using measured soil water retention data and calibrated using field data collected over a 596-d period. The orchard was found to be profoundly leaky with between 15 and 33% of the average annual rainfall being lost via runoff and deep drainage under rainfed conditions. Simulations estimated that the current management of the young trees resulted in loss of 38.1 kg N ha1 yr1 or 46% of the applied nitrate, and 34.6 cm yr1 of rainfall and irrigation as drainage below 2.0 m depth. For mature trees, our model scenarios predicted that converting from sprayers to drippers, would reduce the required irrigation by 44%, reduce nitrate requirement by 21%, and reduce deep drainage and nitrate leaching by 37%. Deficit-based irrigation and fertigation scheduling had minimal effect on the amount of deep drainage and nitrate leaching. In mature trees, excluding green fowl manure from the fertilizer regime was predicted to reduce the amount of nitrate leached below the soil profile by 12.9 kg N ha1 yr1 or by 73%. However rates of NPK and fertigation needed to be increased to meet tree nitrogen demand.