Hypoxic blackwater floods constitute a major disturbance event in aquatic ecosystems. Zooplankton are generally considered to be relatively resistant to hypoxic conditions, however their responses to hypoxia instigated by blackwater floods have been rarely examined. In this study we monitored the response of zooplankton to the 2013 hypoxic blackwater event in the Hunter River estuary. Major shifts in zooplankton abundance and assemblages occurred during and following the event. Prior to the flood copepods were dominated by the calanoid Galdioferens pectinatus, during the event these were replaced by the cyclopoid Mesocylops sp., and in the months after adults had been replaced largely by copepodites and high numbers of nauplii. Cladoceran populations shifted from a relatively small but diverse assemblage dominated by daphnids to larger populations almost exclusively of Moina sp. and Bosmina meridionalis, before declining in the months after the event. Rotifer abundance declined during the event however increased significantly afterwards, dominated by high numbers of Polyarthra, Filinia, and Brachionus. Whilst the event significantly impacted zooplankton communities, it appeared different genera were able to take the place of those displaced. The results provide insight into the food resources available to higher trophic organisms repopulating estuaries following hypoxic blackwater events.