The rise of ground water and salinity persist as potential challenging issues across irrigated agricultural landscapes. Additional water from irrigation may cause mobilisation of stored salts with subsequent local and off-site salinisation problems. Shallow root systems (<2 m) of irrigated annual crops such as cotton result in less extraction from deeper soil layers (than the original native vegetation). Also, unlike perennial native vegetation, annual crops generally do not utilize rainfall ex-growing season (Williamson 1973). Deep drainage (DD) - water that passes beyond the root zone - can be an important contributor in terms of recharging ground water as well as leaching salts from the root zone. However, DD may also contribute to rising ground water tables with increased solute concentrations. Although cotton is generally regarded as a salt tolerant plant, yield decline commences with electrical conductivity values above 7.7 dS/m with a 50% reduction in yield at 17.0 dS/m (Lin et al., 1997; Ahmad et al. 2002). In the past, water balance studies have focused mainly on infiltration, run-off and soil conservation (Freebairn et al. 1996). However, agricultural industries such as the Australian cotton industry have become increasingly aware of water losses due to DD in the furrow irrigated, heavy textured soils (Vertosols) where furrow lengths often exceed 800 m (Silburn et al. 2004). While the prime aim of the project was to directly quantify DD, a secondary aim was to monitor irrigation application efficiencies in terms of current irrigation methods. To this end, the study has been investigating the comparative efficiency of a lateral move irrigator vs furrow irrigation, in terms of lessened water applied and DD. Lateral moves (LM) are considered by many in the cotton industry as having great potential for positive impacts on water savings. More generally, Wiggington (2008) discusses the different influences on irrigation performance that will also impact quantities and temporal changes in DD, including infiltration characteristics, inflow rate, field length, soil water deficit and field slope.