Seawater intrusion into coastal aquifers poses a significant threat to groundwater resources, especially with rising sea levels due to climate change. Accurate modeling and uncertainty quantification of this process are crucial but are often hindered by the high computational costs of traditional numerical simulations. In this work, we develop GeoFUSE, a novel deep-learning-based surrogate framework that integrates the U-Net Fourier Neural Operator (U-FNO) with Principal Component Analysis (PCA) and Ensemble Smoother with Multiple Data Assimilation (ESMDA). GeoFUSE enables fast and efficient simulation of seawater intrusion while significantly reducing uncertainty in model predictions. We apply GeoFUSE to a 2D cross-section of the Beaver Creek tidal stream-floodplain system in Washington State. Using 1,500 geological realizations, we train the U-FNO surrogate model to approximate salinity distribution and accumulation. The U-FNO model successfully reduces the computational time from hours (using PFLOTRAN simulations) to seconds, achieving a speedup of approximately 360,000 times while maintaining high accuracy. By integrating measurement data from monitoring wells, the framework significantly reduces geological uncertainty and improves the predictive accuracy of the salinity distribution over a 20-year period. Our results demonstrate that GeoFUSE improves computational efficiency and provides a robust tool for real-time uncertainty quantification and decision making in groundwater management. Future work will extend GeoFUSE to 3D models and incorporate additional factors such as sea-level rise and extreme weather events, making it applicable to a broader range of coastal and subsurface flow systems.