Effects of waterlogging were studied in the field and under glasshouse conditions on two clonal lines of Eucalyptus camaldulensis Dehnh (river red gum), which are used in the rehabilitation of damaged agricultural catchments in Western Australia. The plantation of 9-year-old trees was in a position that covered a range of waterlogging and salinity conditions. Up-slope the water table was deeper (0.65–1.5 m), whereas the water table was closer to the ground surface down-slope (0.45 m in winter; 1.25 m in summer). Salinity was greater downslope and increased at the end of the dry summer, remaining high until diluted by the winter rains. Trees of both clonal lines were smaller downslope and used less water over the year. Clone M80 used more water in winter; clone M66 more in summer. In the field, the roots of clone M80 were evenly distributed through the soil profile, while roots of clone M66 decreased with increasing depth. Production of new root terminals varied with season. Greatest production was in spring and early summer, with much lower production over late autumn and winter. Only clone M66 produced new root terminals at depth (60–75 cm) during the drier months of late summer and early autumn. At this time, saline ground-water was the main source for water uptake. To explore clonal differences more closely, the effects of prolonged waterlogging were studied under glasshouse conditions. Clone M80 grew similarly under freely drained and continuously waterlogged conditions for the experimental period (21 weeks). The response under continuously waterlogged conditions was achieved through adventitious root production. By contrast, growth of clone M66 was suppressed under continuous waterlogging, a response associated with the lack of adventitious root production. The results from field and glasshouse studies suggest that clone M80 is more adapted to waterlogging by relatively fresh water than clone M66, but that clone M66 may use water of higher salinity than clone M80. Clone M80 would be better suited to higher positions in partially cleared catchments, where rainfall provides relatively fresh soil water. Clone M66 is better suited to lower catchment positions due to its ability to utilize more saline groundwater. Restoration of the water balance of damaged agricultural catchments can be best managed by matching specialized genotypes with particular catchment positions.