1. Estuarine wetlands are important nurseries for fish and decapod crustaceans. Flood mitigation structures (such as levees, culverts and floodgates) that fragment wetland habitat can reduce fish and crustacean passage and subsequently impact biodiversity.
2. Remediating structures to enhance connectivity, tidal flushing and fish and crustacean passage are assumed to be important ways to rehabilitate estuarine wetlands, but they are rarely evaluated with a robust sampling protocol. Furthermore, studies are inconsistently applied across different barrier types, and success is variable. Consequently, those rehabilitating wetlands are left with an incomplete understanding of what trajectories of change (if any) may be expected from barrier remediation.
3. In collaboration with landholders and managers, ‘floodgate remediation’ (structural and operational changes to increase tidal flushing and connectivity) was undertaken in three tidal creeks in two coastal river systems in northern New South Wales, Australia. Changes in fish and crustacean passage were measured for two different techniques (flap gates built into larger gates and the intermittent opening of gates with manual winching) using a BACI design over 2 years. Temporal changes in assemblages and species richness in managed creeks were compared to those in reference creeks (i.e. without floodgates) and control creeks (with closed floodgates).
4. Both types of floodgate remediation enhanced the passage of fish and crustaceans and had significant impacts on assemblages in managed creeks when compared to control and reference creeks. This shift was sustained for the duration of our study in two of the three creeks and was driven primarily by an increase in the number of estuarine–marine-dependent species.
5. Synthesis and applications. Our study demonstrates that floodgate remediation can facilitate fish and crustacean passage and rehabilitate aquatic assemblages in defaunated, tidally restricted wetlands. Given that the vast majority of floodgates throughout south-eastern Australia can be altered to promote connectivity, such remediation may play an important part in guarding against future declines in estuarine connectivity arising from climate change.