Increasing coastal risks and habitat losses have increased the interest in nature-based solutions for coastal protection. As such managed realignment (MR) is often presented as a win-win solution in rural areas. However, the level of coastal protection that MR can offer now and under climate change is still unclear. Evidence at the estuarine scale is scarce and existing studies rarely account for interactions between river discharge, tides and storm surge. We use a numerical model to assess estuarine-scale impacts of the Hesketh Out Marsh MR (UK) for storms scenarios under present and future sea level rise (SLR) conditions. Our scenarios were defined through repeated interactions with local actors and include river and ocean drivers combinations not previously explored. Results show that MR impacts are highly localised, spatially variable and storm dependent. The MR can reduce total water levels (TWL) upstream of the MR for storms on spring tides and reduce tidal range and surge. However, it can also have unintended consequences such as increasing inundation time opposite to the MR and raising TWL for storms on neap tides, low water levels (LWL) and river-induced water levels. SLR further amplifies these impacts by reducing TWL and increasing LWL as SLR increases. Our results suggest the MR ability to reduce water levels in estuaries may be overestimated when compound river-coastal extremes are not considered and underscores the need for comprehensive modelling and local engagement to achieve effective mitigation and adaptation at estuarine scale.