Estuarine storm surge barriers are designed to prevent the flooding of human-developed landscapes. While such barriers may have a range of ecological impacts, including the fragmentation of aquatic habitats and the alteration of water quality, their impact on obligate estuarine fishes is largely unknown. The sparid, Acanthopagrus butcheri, was used as a model species to determine how surge barriers may influence the movements of solely estuarine species and fish kill events. Individual A. butcheri were monitored for one year using passive acoustic telemetry in the Vasse-Wonnerup Estuary (south-western Australia), in which fish kills occur regularly during summer and autumn. Hydrological data and surge barrier operational information were used to make inferences on the movements and habitat use of A. butcheri. Individuals were largely restricted to the waters downstream of the surge barriers. The fish tended to occupy deeper sites in proximity to complex structure with the distribution also influenced by changes in salinity during the spawning period. A strong seasonal trend existed in the daily distance travelled by the fish and this was positively associated with the annual flow period. The majority of fish that successfully passed upstream through one of the surge barriers did so through a fishgate that operated outside of the spawning period. All those fish were then likely trapped with no downstream fish passage occurring in summer and autumn at a time when water quality was characterised by low dissolved oxygen and cyanobacterial blooms. The surge barrier therefore acts as a seasonal trap and increases the risk of mass mortalities. Given a projected increased need to combat flooding and storm surges associated with climate change in low-lying coastal areas, the study highlights the necessity of ensuring that the life-cycles and movement requirements of estuarine fishes are considered in the design and operation of coastal flood mitigation structures.