AbstractIn this study, we apply probabilistic estimates of mean sea level (MSL) rise and a sub-set of regional climate model ensemble simulations to force a numerical model of the southern North Sea, downscaling projected sea level variability to the Elbe estuary that serves as a prototype for an industrialised meso-tidal estuary. The specific forcing combination enables a localised projection of future estuarine hydrodynamics accounting for the spread of projected global sea level rise and the spread of the regional climate projection due to internal variability. Under the applied high-emission scenario, the Elbe estuary shows high decadal rates of mean water level (MWL) rise beyond 19 mm y-1, increase in the tidal range of up to 14 mm y-1 and increase in extreme water levels of up to 18 mm y-1. The bandwidth of the estuarine response is also high. For example, the range of average monthly extreme water levels is up to 0.57 m due to the spread of projected global sea level rise, up to 0.58 m due to internal variability whereas seasonal range attains 1.99 m locally. In the lower estuary, the spread of projected global sea level rise dominates over internal variability. Internal variability, represented by ensemble spread, notably impacts the range of estuarine water levels and tidal current asymmetry in the shallow upper estuary. This area demonstrates large seasonal fluctuations of MWLs, the M2 tidal amplitude and monthly extreme water levels. On the monthly and inter-annual time scales, the MWL and M2 amplitude reveal opposite trends, indicative of a locally non-linear response to the decadal MSL rise enforced at the open boundary. Overall, imposed by the climate projections decadal change and MSL rise enhance the horizontal currents and turbulent diffusivities whereas internal variability locally mitigates sea level rise–driven changes in the water column. This work establishes a framework for providing consistent regionalised scenario-based climate change projections for the estuarine environment to support sustainable adaptation development.