Extreme low and high flow periods associated with droughts and floods regularly influence many river system, yet little is known regarding their role in shaping riverine zooplankton communities. This study investigated zooplankton dynamics in response to the transition from drought to flooding in four southern Murray–Darling Basin rivers managed by different levels of flow regulation. Results indicated that the onset of flooding was associated with an increase in the taxon richness and total transport (abundance) of zooplankton in the unregulated Ovens and Kiewa Rivers, and an increase in the total transport of zooplankton in the mildly regulated Broken River. In comparison, no significant flood effects on zooplankton taxon richness or transport were detected in the highly regulated Murray River. This suggests that the flooding was beneficial for enhancing zooplankton abundance in the Ovens, Kiewa and Broken Rivers, whereas any potential benefits were comparatively short-term and/or reduced in the Murray River. We hypothesise that the relatively short-term and/or reduced response of the zooplankton community to the flooding in the Murray River was probably largely due to the occurrence of a hypoxic blackwater event in suppressing zooplankton emergence.