Seedling establishment typically represents a significant bottleneck in the population dynamics of trees and shrubs in riparian and floodplain habitats of inland Australia (e.g. George et al., 2005; Thoms et al., 2007). Woody riparian species of semi-arid and arid regions often produce large numbers of seeds that typically germinate rapidly and opportunistically (e.g. Streng et al., 1989; Chong and Walker, 2005). The survival of seedlings in these hydrologically variable habitats, however, tends to be low and patchy, both spatially and temporally (Streng et al., 1989; Hughes, 1990; Cooper et al., 1999; Horton and Clark, 2001). Knowledge of the factors influencing seedling survival is therefore critical to understanding vegetation dynamics in these environments.Vegetation structure in semi-arid and arid riparian and floodplain habitats is usually governed by the unpredictable patterns of flooding and drying that characterise these environments (e.g. Stromberg 2001; Brock et al., 2006). Hydrology also tends to have an overriding effect on seedling growth and survival in riparian habitats (e.g. Cooper et al., 1999; Horton and Clark, 2001; Capon et al., 2009). Seedlings are typically more vulnerable to the stresses imposed by flooding and drought than mature plants due to their smaller size (Cooper et al., 1999; Gindaba et al., 2004). Flooding can have a direct influence on seedlings through soil anoxia and toxicity, reduced light, mechanical damage and burial but may also provide structural support (Blom et al., 1990; 1996). The magnitude of these flood-induced effects are likely to vary with seedling size and developmental stage as well as flood characteristics such as depth, duration and timing (e.g. Capon et al., 2009). In arid systems, floodwaters also provide an important source of soil moisture during periods of flood recession which may favour seedling growth. The rate of drawdown of the water table can therefore be an important influence on the survival of seedlings into subsequent dry periods (Horton and Clark, 2011).