Using high-resolution, ensemble-based modeling of the CMIP6 High Resolution Model Intercomparison Project, this study evaluates potential changes to extreme coastal water levels and waves across the Salish Sea, the largest estuary on the North American west coast. Results of a well-validated (water level error ~10 cm) regional hydrodynamic and wave model indicate that extreme water levels (e.g., 30-year return period) are projected to increase across the region, while lower-magnitude events (e.g., annual) are projected to slightly decrease. Wave height projections are spatially heterogeneous but generally decrease in southern basins and increase in the far north basins. Seasonal decomposition reveals a modest decrease in winter water levels and an increase in summer water levels. Non-linear interactions between sea level rise (SLR) and hydrodynamic response were assessed across seven SLR scenarios (0–3 m), revealing localized amplification effects up to 10 cm, though these remain minor relative to the SLR signal. Overall, uncertainty across the CMIP6 ensemble is high in this region, rendering most modeled changes statistically non-significant and emphasizing the need for studies to consider an ensemble when looking at climate projections. The dominance of tidal forcing in extreme water levels, coupled with high inter-model variability, indicates that near-term climate-induced changes to oceanic drivers are unlikely to significantly alter coastal hazards in the Salish Sea by 2050. These findings support the use of present-day conditions as a proxy for near-future planning and emphasize SLR as the primary contributor to changing future coastal risk in the Salish Sea.