Variable groundwater quality in complex aquifer-aquitard systems presents a challenge for sustainable groundwater development. In the Lower Murrumbidgee alluvial fan of the Murray-Darling Basin in semi arid inland Australia, shallow groundwater is saline (12000 &micro S/cm) and locally contaminated by nitrate. Deep fresh aquifers (150 &micro S/cm), developed as an irrigation water supply, were thought to be protected from downwards leakage by laterally extensive aquitards. However, hydrochemical sampling, augmented by historic data, revealed that aquifer salinisation (400 to 4000 &micro S/cm) had occurred at some sites to 50 m depth since the mid 1980s. Aquitard windows, landscape depositional features at a scale of 10s to 100s of metres which are rarely detected by conventional investigations, were proposed as conduits for rapid downwards leakage in stressed systems. Intensive research was conducted at the Tubbo site where downhole geophysical logging and minimally disturbed cores were used to describe a saline clayey silt to 15m depth, an indurated clayey sand and 2 deep deposits of hard clayey silt. Fracturing was inferred by the scale dependency of aquitard permeability (Kv 10E-11 to 10E-6 m/s). Lithological variation near the surface was delineated by electrical imaging which revealed a 40m wide aquitard window beneath a veneer of smectite clay. Intensive monitoring of groundwater pressures in six piezometers (23-96 m depth) near the Tubbo irrigation bore and two other peizometers upgradient, indicated that the indurated clayey sand formed an effective hydraulic barrier but the deep silty deposits were spatially discontinuous. Groundwater samples were collected before, three times during, and after the 1998-99 irrigation season. A large, but delayed TDS increase occurred in the shallow aquifer and small pulses of saline water were sustained in the middle aquifer but shortlived in the deep aquifer. Hydrochemical and isotopic data dC-13, dH-2, dO-18, C-14 and H-3) showed the middle aquifer mixing with the deep aquifer, though retaining the signature of a palaeowater. Hydrochemical changes were accounted for with PHREEQC inverse mass balance models for the shallow aquifer. Mixing of aquifer water with 20-70% saline porewater from the upper aquitard occurred, together with ion exchange and NaCl dissolution. Based on an axisymmetric radial FEFLOW model, 5-30% of the volume pumped was accounted for by vertical leakage from the middle aquifer. Leakage from the shallow aquifer was small but significant, as it allowed high salinity water to migrate. Permeability and compressible storage measurements (Ss 10E-5 to 10E-4 /m) were used to constrain model calibration, and to show that direct mixing occurred mainly via aquitard windows at depth, and between the shallow and middle aquifers via leaky boreholes. Fracture flow and aquifer-aquitard interaction by diffusion were of secondary importance.