The structure and dynamics of fish assemblages were studied in two small coastal streams in the seasonal tropics of northern Queensland. The study encompassed two consecutive wet seasons of contrasting flood magnitudes. Flooding had substantial effects on physical habitats by shifting sediments and removing aquatic macrophytes, and short-term changes in the fish assemblages reflected these habitat changes. Changes were of higher magnitude following a one-in-eighteen-year flood than a one-in-one-year flood; however, in both cases return to prior assemblage structure occurred as the dry season progressed, but with more rapid recovery after the smaller event. The stream fish assemblages showed high resilience to the flood disturbance at magnitudes seen in this study.