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The responses of algal assemblages in and zone rivers to flow events, drying and water quality changes are fundamental to our understanding of these unregulated rivers. We studied planktonic and other algae, identified to genus, in three rivers in the Lake Eyre Basin. where summer-autumn floods typically occur on an annual basis. A moderately diverse algal flora was discovered with a total of 118 genera, containing at least 237 taxa, in seven phyla. Algal diversity was found to be highest during, or soon after flood events of varying sizes and in the summer following a large flood in the previous flood season. We suggest that the combination of germination of algae from channel and floodplain sediments and the transport of algae from aquatic refuges during flood events resulted in the observed increases in diversity. In addition, nutrient influxes associated with previous large floods, interact with the increase in temperature in the subsequent summer to provide optimum conditions for high algal production and, in some sites, high diversity. Multivariate analyses found that salinity was a significant driver of assemblage composition but only explained a small portion of the variance in generic richness. Within phyla, assemblage richness within the Chlorophyta and Euglenophyta showed a weak, but significant, negative correlation with increasing salinity, while in the Cyanophyta and Bacillariophyta richness was not significantly correlated because both latter groups contained salt-tolerant taxa. Copyright (c) 2005 John Wiley T Sons, Ltd.