The purpose of this study was to assess the distribution of early life stages of fish (fish fry) across different seasonal floodplain types; primary, secondary and rarely flooded floodplains in the Okavango Delta. This was of importance as the flood pulsing nature of the Okavango Delta is threatened by proposed water developmental projects and climate change. Thus, the system might lose connections to some of its floodplains such as the rarely flooded floodplains that get inundated under high floods and they might dry permanently. Field sampling was conducted during the flood rising phase (May 2009, March 2010, May 2010), flood peak (July 2009, October 2009, June 2010) and during the flood recession phase (February 2010). Physical water parameters were measured in situ whilst fish were surveyed using a throw-ring net and standardised scoop netting. The rarely flooded floodplains recorded the significantly highest levels of turbidity and dissolved oxygen. Fish from 38 fish taxa belonging to 11 families were identified and classified during the study. The small fish species were significantly abundant in the primary floodplains whilst the rarely flooded floodplains characterised by high turbidity were dominated by cichlids. The analysis of both physicochemical water parameters and fish fry pointed out to spatio-temporal variations across different floodplain types.