The salinity and its longitudinal distribution in the Weser estuary, Germany, has implications for water management as the estuarine water is needed, e.g., for irrigation of the agricultural used hinterlands and as industrial water and because of its intrusion into groundwater. Generally, the salinity distribution is determined by tidal dynamics, river runoff from the catchment area, amount of intruding seawater from the German Bight (North Sea) as well as by the salinities of both river and seawater. Anthropogenic climate change may have an impact on the estuarine dynamics and, thus, on the salinity distribution. This study focuses on the impact of storm surges. A semi-implicit Eulerian-Lagrangian finite element model was used to simulate hydrodynamics and salinities in the estuary. By comparing simulated and observed data of two past storm surges it is shown that the model is well capable of reproducing estuarine dynamics. Possible future changes due to climate change are investigated for three scenario-based storm surges; two of them represent future storm conditions and one specifies reference (today's) conditions for comparison. These storm surges were simulated using boundary conditions from water level simulations with a hydrodynamic model for the North Sea together with the respective meteorological forcing. It can be shown that during storm tides, isohalines penetrate more than 30km further upstream than during normal conditions. For the most severe scenario-based storm surge, this leads to a salinity increase of up to 30psu within the mixing zone during the highest storm tide.