Communities exposed to intermediate disturbances have been shown to be more diverse than more stable or unstable systems. We recorded the diversity pattern of zooplankton in the Okavango Delta, Botswana, a system which include water bodies with different stability with regard to water levels and wet-dry phases, from permanent rivers and lagoons to seasonal floodplains and temporary water-filled rain ponds. The yearly flood pulse caused a gradual shift in aquatic parameters on seasonal floodplains, which promoted zooplankton diversity. Species composition differed between temporal and permanent habitats, but highest diversity was recorded on floodplains. Diversity on floodplains showed a distinct seasonal trend, being low during increasing flood, to highly diverse during high water periods. Density and hatching sequence of major cladoceran species suggested that the bank of resting eggs in the soil is the major source of species occurrence during flooding. We propose that seasonal floodplains, which have significant higher diversity and abundance, serve as source areas for the cladoceran diversity in the Okavango Delta. From these habitats ephippia are dispersed into the other four habitats. The dominant vectors for such dispersal are probably wind and mammals.