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The flow regime of Cooper Creek, central Australia, is subject to a summer-monsoonal climate and aseasonal cycles associated with the El Nino-Southern Oscillation (ENSO). Analysis of a 48-year hydrograph indicates that floods tend to occur in clusters associated with La Nina episodes. The influence of ENSO is apparent in lagged correlations between discharge and values of the Southern Oscillation Index (SOI), and in measures of coherency derived from cross-spectrum analysis. Hydrological persistence is indicated by partial auto-correlations between floods in successive years. In a cluster of five floods over 1987-1991, cumulative effects were apparent in wetland habitat areas, in water temperature and transparency, and in the recruitment patterns of five fish species: Nematalosa erebi (Clupeidae), Hypseleotris klunzingeri (Gobiidae), Melanotaenia splendida tatei (Melanotaeniidae), Retropinna semoni (Retropinnidae) and Gambusia holbrooki (Poeciliidae). During serial floods, native fish appear to have a recruitment advantage over the exotic Gambusia. Hydrological persistence and its ecological correlates warrant consideration in research, planning and management, particularly in regard to the water resources of arid and semi-arid regions. Copyright (C) 2000 John Wiley & Sons, Ltd.