The response and recovery of aquatic ecosystems to major flooding is directly associated with the resistance and resilience of the perturbed ecosystem. In this 2-year study, we document the response of taxa assemblages in five tributary creeks of the Clarence River, Australia, following two sequential floods. Prior to the floods, we observed clear differences of taxa assemblages among tributaries, and clear but relatively small seasonal changes in all creeks. Flooding triggered large shifts in taxa assemblages in all creeks; however, only a few species out of the 106 taxa analysed were contributing to this pulse response. Combinations of specific water quality variables were significantly associated with the observed patterns in taxa assemblages in all but one creek. After an initial rapid recovery period, taxa compositions in all tributaries more slowly returned to resemble those before the floods. This strong resilience to major floods is most likely associated with high flushing rates, spatial and temporal refugia and life history characteristics of key biota. Overall, the results suggest that the current state of the Clarence floodplain has achieved a strong resilience to major flood disturbances, and that a shift to an alternate, potentially more desirable state may be difficult to achieve.