This data set consists of physics-based Delft3D-Flexible Mesh hydrodynamic model input files that are used to simulate compound flood exposure of the lower Nooksack River and delta of western Washington State under existing and future conditions of anticipated climate and land-use change. The model enables assessment of the changing flood exposure associated with the cumulative impacts of expected sea-level rise, greater tidal inundation, more frequent storm surge effects, and higher winter stream floods in the 2040s and 2080s. The model also accounts for proposed flood mitigation strategies, and recently observed decadal climate-driven sedimentation patterns. Example model input and configuration files are included for the base 2020 flood and the 2020 flood under the 2080s high change scenario and alternative 3B flood mitigation strategy.