Tidally-active wetlands are important nursery grounds for juvenile fish and decapod crustacean species, but urban development has significantly reduced their availability. Structural flood mitigation works, such as installing culverts and floodgates, have been responsible for a lot of this decline. These works fragment habitat, restrict tidal flushing and degrade nursery habitat of estuarine fish and decapod crustaceans (collectively referred to as nekton). Such losses cannot occur without associated losses in the productivity of fisheries. The findings of the current study provide evidence that at least some of these declines may be reversible if rehabilitation projects are adaptively managed over sufficiently long time periods. The incremental opening of eight floodgates at Hexham Swamp adjacent to the Hunter River in New South Wales, afforded the rare opportunity to monitor water quality and nekton assemblages in a tidal creek over an extensive (eleven year) period encompassing pre-floodgate opening, the opening of one gate, three gates and finally all eight gates. Floodgate opening enhanced both water quality and nektonic assemblages relative to a control creek whose barrier remained in place. However, recovery to a state similar to unrestricted reference creeks was not immediate and did not occur until after all eight gates were opened. This case study serves to stress the importance of reinstating tidal flushing to nursery habitats in order to enhance populations of economically valuable coastal fish and decapod species, and moreover, that increasing levels of tidal flushing may need to be incrementally applied in some systems before a threshold response in recovery is achieved.