The regulation of Australian lowland rivers such as the River Murray has resulted in changes to the flooding characteristics of many associated wetlands. It has been suggested that these changes in flooding have changed the pattern of response of many wetland biota. The substantial variability in the size and shape of these wetlands makes limited field observations difficult to interpret. To overcome this variability 16 experimental billabongs were constructed in which factors that may cause changes to populations within billabongs could be manipulated. In this paper we report on experiments that test the hypothesis that changing the pattern of flooding alters the density and diversity of rotifers and microcrustaceans in billabongs. The experimental billabongs were sampled fortnightly for two years. During this time four flood events were imposed. Flooding of the experimental billabongs resulted in increased microcrustacean abundance. Rotifer abundance rarely increased following flooding. Changing the time of flooding did not modify this response. Observed changes in community structure following flooding result from changes in the relative densities of taxa already present rather than changes in the community composition.