The Puget Sound Coastal Storm Modeling System (PS-CoSMoS) is a tool designed to dynamically downscale future climate scenarios (i.e., projected changes in wind and pressure fields and temperature) to compute regional water levels, waves, and compound flooding over large geographic areas (100 s of kilometers) at high spatial resolutions (1 m) pertinent to coastal hazard assessments and planning. This research focuses on advancing robust and computationally efficient approaches to resolving the coastal compound flooding components for complex, estuary environments and their application to the Puget Sound region of Washington State (USA) and the greater Salish Sea. The modeling system provides coastal planners with projections of storm hazards and flood exposure for recurring flood events, spanning the annual to 1-percent annual chance of flooding, necessary to manage public safety and the prioritization and cost-efficient protection of critical infrastructure and valued ecosystems. The tool is applied and validated for Whatcom County, Washington, and includes a cross-shore profile model (XBeach) and overland flooding model (SFINCS) and is nested in a regional tide–surge model and wave model. Despite uncertainties in boundary conditions, hindcast simulations performed with the coupled model system accurately identified areas that were flooded during a recent storm in 2018. Flood hazards and risks are expected to increase exponentially as the sea level rises in the study area of 210 km of shoreline. With 1 m of sea-level rise, annual flood extents are projected to increase from 13 to 33 km² (5 and 13% of low-lying Whatcom County) and flood risk (defined in USD) is projected to increase fifteenfold (from 14 to USD 206 million). PS-CoSMoS, like its prior iteration in California (CoSMoS), provides valuable coastal hazard projections to help communities plan for the impacts of sea-level rise and storms.