We examined the response of nutrient concentrations to the drying and re-flooding of ephemeral deflation basin lakes (EDBL) in western New South Wales, Australia. As lakes dried total nitrogen (TN) and total phosphorus (TP) concentrations increased. TN concentrations increased more quickly and TP concentrations increased more slowly than could be attributed to evaporation alone. This suggested that additional nitrogen was being sequestered from the atmosphere or sediments and that some phosphorus loss to the sediments was occurring. Concentrations of nitrogen oxides (NOx) and filterable reactive phosphorus (FRP), however, declined as lakes dried, suggesting a tighter coupling of nutrient release and uptake mechanisms. Inorganic nutrient concentrations rose sharply in response to re-flooding in all lakes. Evidence is provided to suggest that post-flood nutrient pulses are the net result of both riverine inputs and sediment releases and that the relative significance of either may be influenced by regulation.