A numerical hydrodynamic model is used to investigate the sensitivity of a morphologically complex and heavily “engineered” mesotidal estuary to idealized sea-level rise scenarios and to evaluate the appropriateness of managed realignment as an adaptive response to sea-level rise. The hydrodynamic regime of the Blyth estuary (Suffolk, eastern England) is governed by a distinctive morphology that has resulted from the abandonment of a reclaimed midestuary tidal floodplain in the 1920s and 1940s. Hypsometric characteristics (extensive intertidal area and constricted inlet dimensions) make the outer estuary potentially sensitive to sea-level rise. Model results indicate that a sea-level rise of 0.3 m (as a best estimate scenario for 2050) could increase peak tidal current velocities and discharges by up to 20% and 28%, respectively. Extensive areas of potential tidal floodplain remain protected by embankments that will require upgrading to cope with sea-level rise. Realignment (or “managed retreat”) of these defences can reduce local flood defence costs by eliminating unsustainable seawall but needs to be evaluated in the light of wider impacts. Modelling of hypothetical realignment scenarios shows that restoration of tidal exchange to the largest flood compartments could have an immediate effect on outer estuary hydrodynamics that is larger than worst case scenarios for half a century of accelerated sea-level rise (peak velocity and discharge increased by up to 35% and 32%, respectively). More generally, incompatibilities are apparent between flood defence and habitat restoration objectives, such that the appropriateness and feasibility of large-scale flood defence realignment could be questionable in estuarine contexts.