A bio-physical modelling study is presented which simulates the drainage under an annual clover and a perennial lucerne pasture. The simulations are compared with measurements taken at a trial near Katanning, Western Australia, subject to a Mediterranean climate. The results show the water balance of the site to be dominated by the vertical dimension, with no apparent lateral flow in the B soil horizon. Drainage under lucerne was found to be less than that under the clover during the growing season of the annual pasture. However, our results suggest the dominant drainage control may be site and soil characteristics rather than pasture type. We found that using measured values of hydraulic conductivity led to much higher drainage than could be supported by observations of perched watertables within the A and B horizons. The observations suggest that the subsoils change their structure when they moisten in winter and become much less conductive. In order to model the site, a soil profile had to be invoked which reflected field water table hydrograph observations rather than soil water characteristics determined in the laboratory or from field profile texture observations.