This study examines the applicability of the assumption in flood frequency analysis that flood peaks are independent and identically distributed. It investigates the effect and extent of multidecadal variability for mainly coastal, eastern Australian flood data. The Interdecadal Pacific Oscillation (IPO) is a climate index which describes this long-term variability. The flood data were stratified by IPO value and flood frequency analyses performed. Analysis of the stratified flood distributions revealed that the IPO modulated the flood risk in New South Wales and southern Queensland, with flood quantiles being increased by a factor of approximately 1.7 during IPO negative periods, whereas little effect was detected for sites in north-east Queensland located approximately north of the Tropic of Capricorn. This IPO modulation of flood risk may be explained by multidecadal movements of regional convergence zones. Neglect of the IPO dependence on flood risk can lead to significant bias in long-run flood risk.