Ecological responses to wetting and drying in dryland river floodplain systems are often described in terms of “boom” and “bust”. We suggest that patterns in floodplain species abundances and assemblage structures will be closely linked to the changes in spatial habitat heterogeneity that accompany flooding and drying phases. This study examined the responses of zooplankton through a wetting and drying cycle in a complex floodplain-wetland system in semi-arid Australia, the Narran Lakes. We illustrate the complexity of the zooplankton “boom” and “bust” response. Total densities of zooplankton varied considerably over time and patterns were very dissimilar between sites with abundances varying from <30 animals/L to over 4000 animals/L. We detected different patterns in the proportion of variance in abundances of the broad taxonomic groups (rotifers, cladocerans, ostracods, calanoid copepods, cyclopoid copepods and nauplii) explained by time and space. Site explained the highest proportion of variation in cladoceran and ostracod abundances,whereas variance in calanoid abundances was explained predominantly by time since inundation. Variation in the abundances of the remaining groups was explained largely by the site by time interaction. Zooplankton assemblages were observed to diverge during drying with highest between-site dissimilarities in assemblage structure occurring during the later stages of drying. Such high spatial and temporal variability in zooplankton abundances and community composition could have important consequences for consumers such as fish and some wetland birds that utilize these ephemeral systems for feeding and breeding while they are inundated.