In the current context of climate change, understanding the effects of the changing conditions on estuaries is of utmost importance to protect populations and ecosystems. Given the diversity of impacts depending on the region, there is a need for local and dedicated studies to understand and mitigate the risks. Numerical models can provide forecasts of extreme floods and sea-level rise (SLR). However, they can present inaccuracies. In this work, the ensemble technique was applied to improve the numerical modeling forecasting for estuaries by considering scenarios of extreme river flow discharges (EFDs) and SLR scenarios for 2050 and 2100. The simulations were performed for two different estuarine regions in northern Portugal, and the superensemble was constructed with the results of two different numerical models. The results differed per estuary, highlighting the importance of a local approach. For the Douro estuary dynamics, the results showed that for the EFD, the effects of the SLR were not noticeable, indicating that, in this estuary, the river component was more important than the maritime component. In contrast, the Minho estuary dynamics were found to be affected by the SLR along the whole estuarine region, indicating a maritime influence and a worsening of the flood conditions for future scenarios.