Current understanding of the combined effects of sea level rise (SLR), storm surge, and changes in river flooding on near-coastal environments is very limited. This project uses a suite of numerical models to examine the combined effects of projected future climate change on flooding in the Skagit floodplain and estuary. Statistically and dynamically downscaled global climate model scenarios from the ECHAM-5 GCM were used as the climate forcings. Unregulated daily river flows were simulated using the VIC hydrology model, and regulated river flows were simulated using the SkagitSim reservoir operations model. Daily tidal anomalies (TA) were calculated using a regression approach based on ENSO and atmospheric pressure forcing simulated by the WRF regional climate model. A 2-D hydrodynamic model was used to estimate water surface elevations in the Skagit floodplain using resampled hourly hydrographs keyed to regulated daily flood flows produced by the reservoir simulation model, and tide predictions adjusted for SLR and TA. Combining peak annual TA with projected sea level rise, the historical (1970–1999) 100-yr peak high water level is exceeded essentially every year by the 2050s. The combination of projected sea level rise and larger floods by the 2080s yields both increased flood inundation area (+ 74%), and increased average water depth (+ 25 cm) in the Skagit floodplain during a 100-year flood. Adding sea level rise to the historical FEMA 100-year flood resulted in a 35% increase in inundation area by the 2040's, compared to a 57% increase when both SLR and projected changes in river flow were combined.