Deep drainage or drainage below the bottom of the profile usually occurs when rain infiltrates moist soil with insufficient capacity to store the additional water. This drainage is believed to be contributing to watertable rise and salinity in some parts of the Liverpool Plains catchment in northern New South Wales. The effect of land use on deep drainage was investigated by comparing the traditional long fallow system with more intense ‘opportunity cropping’. Long fallowing (2 crops in 3 years) is used to store rainfall in the soil profile but risks substantial deep drainage. Opportunity cropping seeks to lessen this risk by sowing whenever there is sufficient soil moisture. Elements of the water balance and productivity were measured under various farming systems in a field experiment for 4 years in the southern part of the catchment. The experimental results were used to verify APSIM (Agricultural Production Systems Simulator) by comparing them with predictions of production, water storage, and runoff. The verification procedure also involved local farmers and agronomists who assessed the credibility of the predictions and suggested modifications. APSIM provided a realistic simulation of common farming systems in the region and could capture the main hydrological and biological processes. APSIM was then used for long-term (41 years) simulations to predict deep drainage under different systems and extrapolate experimental results. The results showed large differences between agricultural systems mostly because differences in evapotranspiration contributed to differences in profile moisture when it rained. The model predicted that traditional long fallow farming systems (2 crops in 3 years) are quite ‘leaky’, with average annual deep drainage of 34 mm. However, by planting crops in response to the depth of moist soil (opportunity or response cropping), APSIM predicted a much smaller annual drainage rate of 6 mm. Opportunity cropping resulted in overall greater water use and increased production compared with long fallowing. Furthermore, modelling indicated that average annual deep drainage under continuous sorghum (3 mm) is much less than under either long fallow cropping or continuous wheat (39 mm), demonstrating the importance of including summer cropping, as well as increasing cropping frequency, to reducing deep drainage.