Recent research has highlighted the persistence of multi-decadal epochs of enhanced/reduced flood risk across New South Wales (NSW), Australia. Recent climatological studies have also revealed multi-decadal variability in the modulation of the magnitude of El Niño/Southern Oscillation (ENSO) impacts. In this paper, the variability of flood risk across NSW is analysed with respect to the observed modulation of ENSO event magnitude. This is achieved through the use of a simple index of regional flood risk. The results indicate that cold ENSO events (La Niña) are the dominant drivers of elevated flood risk. An analysis of multi-decadal modulation of flood risk is achieved using the inter-decadal Pacific Oscillation (IPO) index. The analysis reveals that IPO modulation of ENSO events leads to multi-decadal epochs of elevated flood risk, however this modulation appears to affect not only the magnitude of individual ENSO events, but also the frequency of their occurrence. This dual modulation of ENSO processes has the effect of reducing and elevating flood risk on multi-decadal timescales. These results have marked implications for achieving robust flood frequency analysis as well as providing a strong example of the role of natural climate variability.