The decline of riparian vegetation in the lower River Murray, south-eastern Australia, is associated with a reduction in flooding frequency, extent and duration, and increased salt accumulation. The plant water sources of healthy Eucalyptus largiflorens trees growing over highly saline (>40 dS m^–1) groundwater were investigated during summer when water deficit is greatest. The study found low-salinity soil water overlying highly saline groundwater at most sites. This deep soil water, rather than the saline groundwater, was identified as the plant water source at most sites. Stable isotopes of water and water potential measurements were used to infer how the deep soil water was recharged. The low-salinity, deep soil water was recharged in the following two ways: (1) vertically through the soil profile or via preferential flow paths by rainfall or flood waters or (2) horizontally by bank recharge from surface water on top of the saline groundwater. Vertical infiltration of rainfall and floodwaters through cracking clays was important for trees growing in small depressions, whereas infiltration of rainfall through sandy soils was important for trees growing at the break of slope. Bank recharge was important for trees growing within ~50 m of permanent and ephemeral water bodies. The study has provided a better understanding of the spatial patterns of recharge at a scale relevant to riparian vegetation. This understanding is important for the management of floodplain vegetation growing in a saline, semi-arid environment.