Widespread clearing of native vegetation in Southwest Western Australia has led to land degradation associated with rising groundwater, secondary salinisation and waterlogging. Land degradation can be controlled by re-establishing native deep rooted perennial vegetation across parts of the landscape. Alley farming is an agroforestry practice where multiple perennial tree belts are planted in alternation with traditional agricultural crops. To identify the best configuration (belt width verses alley width) for controlling rising groundwater levels and providing viable economic returns, a large scale experiment was established in 1995. The experiment contains seven different alley farming designs, each with transects of piezometers running across tree belts into adjacent alleys to monitor changes in the groundwater level. Two control piezometers were also installed in an adjacent paddock. At the site groundwater is shallow (−1) and so root water uptake from the saturated zone is limited. Simple hydrograph analysis did not identify any treatment effects on the water table response. Subsequent statistical analysis revealed that 20–30% of the variability in the water table data over the 12 year period was attributable to the alley farming experiment. It was hypothesized that a climate trend (reducing annual rainfall over time) may be obscuring the effect of the experiment. To further investigate the effect of the experiment on groundwater response, further hydrograph analysis was conducted to compare the trends in the control piezometers in relation to those located within the belts. A difference of 0.9 m was observed between the mean groundwater levels in the control piezometers and the mean levels in the perennial belt piezometers. For a mean specific yield of 0.03 m3 m−3 this equates to a small additional water use of 27 mm yr−1 by the perennial agroforestry system. It is concluded that declining annual rainfall is the principal control on hydrograph response at the site. Perennial biomass development and perennial root development (both laterally and vertically) exert only a small influence on water table depth. The implications of this study indicate that alley farming has a limited ability to control a rising water table in low lying areas with a shallow saline water table.