1. Zooplankton density and biomass was examined in a Danube River floodplain section with highly variable hydrological dynamics. Temporal patterns were analysed to assess the effects of hydrological conditions on zooplankton community structure and the differential response of the two major zooplankton taxa, rotifers and crustaceans. 2. Calculated floodplain water age was used as an integrated parameter describing hydrological conditions and connectivity. 3. Total zooplankton biomass, crustacean biomass and crustacean species number were significantly positively related to water age. Rotifer biomass followed a hump‐shaped relationship with water age, and rotifer species number decreased with increasing water age. 4. Rotifers dominated the community in periods of low to medium water ages. In periods of higher water ages the community was dominated by crustaceans. 5. We propose that the hydrological regime of floodplains is crucial for zooplankton biomass patterns and succession, through the alternation of washing‐out effects, taxon‐specific potential of reproduction and biological interactions. Flood events and high water levels reset the community to an early successional phase.

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