Estuaries are areas that are vulnerable to the impacts of climate change. Understanding how these impacts affect these complex environments and their uses is essential. This paper presents a work based on an analytical solution and 2DH and 3D versions of the Delft3D numerical model to simulate the Minho River estuary and its saline wedge length under climate change projections. Temperature observations at several locations in the estuary region were selected to determine which model better simulated the temperature patterns. Specific simulations were performed for the observation periods. Sixteen numerical model scenarios were proposed, considering a varying tide, different river flows, and several SLR projections based on the RCP4.5 and RCP8.5 for 2050 and 2100. The analytical solution was also calibrated using the numerical model solutions. The results show that although there is no relevant stratification, there was a difference in both models in which in the worst climate change scenario, the length of the saline intrusion increased up to 28 km in the 2DH model and 30 km in the 3D model. It was concluded that the 3D model results were more precise, but both configurations can provide insights into how the saline intrusion will be affected. Additionally, the excellent agreement between the analytical solution and the results of the numerical models allowed us to consider the analytical solution a helpful tool for practical applications. It was demonstrated that freshwater discharges and bed slopes are the most critical drivers for the saline intrusion length in the Minho River estuary as they have more impact than the increase in sea level. Therefore, flow regulation can be an excellent way to control saline intrusion in the future.