In arid environments, infiltration from ephemeral rivers is believed to be a primary source of groundwater recharge. However, ephemeral river studies have mostly focussed on estimation of transmission loss or riverbed infiltration rates. Where river flows lead to the development of perched aquifers, transmission loss and riverbed infiltration can be much greater than aquifer recharge, as much of the infiltrated water can subsequently be lost to evapotranspiration. The Woodforde River in central Australia has flowed on 34 occasions within the past 16 years. River sediments are highly permeable, but the river is incised into clay sands of lower permeability, leading to the development of a perched aquifer. During an intensively monitored flow, the downstream decrease in river discharge was approximately equal to the volume of the perched aquifer, indicating that infiltration is the main source of river loss during flows. The perched aquifer persists for several months or longer, and water levels decline slowly over time. Comparison between chloride concentrations of river water and soil water from beneath the perched aquifer suggests that 25% of this water leaks through the low permeability sediments to recharge the deep aquifer. The remainder is used by the riparian vegetation or lost to evaporation.