Microcrustacean emergence from the dry sediments is an important colonization pathway that allows these microfauna to recover and repopulate temporary aquatic habitats after months or years of dryness. Viable microcrustacean propagules in sediments of three different temporary aquatic habitats – rainpools located within the rarely flooded portions, frequently flooded floodplains and rarely flooded floodplains – were assessed experimentally by flooding the soils. Three major groups of microcrustaceans – cladocerans, copepods and ostracods – emerged from the sediments. Species richness and mean total numbers of emerged microcrustaceans per sample varied across the studied temporary aquatic habitats (Kruskal–Wallis, p < 0.05). Both species richness and mean total number of emerged microcrustacean per sample were lowest in sediments of rarely flooded floodplains. The highest species richness of microcrustaceans emerged from the treatments with soils of the frequently flooded floodplains. The mean total number of emerged microcrustaceans per sample was highest from sediments of rainpools followed by frequently flooded floodplains. Findings of this experiment suggest that high flooding frequency of temporary aquatic habitats may be important to sustain high viability of microcrustacean propagules in the sediments. Reduction of regular inundation of temporary floodplains due to the threats of increasing human water abstractions and climate change may have some negative effects on the microcrustaceans of the Okavango Delta by reducing the viable propagules within these systems. The findings of this experimental study will be relevant towards efforts that are aimed at reconciling anthropogenic pressures and conservation of microcrustaceans in the Okavango Delta. Copyright © 2012 John Wiley & Sons, Ltd.