These metadata describe the U.S. Geological Survey (USGS), Pacific Coastal and Marine Science Center (PCMSC) merged bathymetry digital terrain model comprised of the 2005, 2007, and 2010 bathymetry data collected in Skagit Bay Washington that is provided as a 1-m resolution TIFF image, as well as a 1-m resolution shaded-relief TIFF image. In 2004, 2005, 2007, and 2010 the U.S. Geological Survey (USGS), Pacific Coastal and Marine Science Center (PCMSC) collected bathymetry and acoustic backscatter data in Skagit Bay, Washington using an interferometric bathymetric sidescan sonar system mounded to the USGS R/V Parke Snavely and the USGS R/V Karluk. The research was conducted in coordination with the Swinomish Indian Tribal Community, Skagit River System Cooperative, Skagit Watershed Council, Puget Sound Nearshore Ecosystem Restoration Project, and U.S. Army Corps of Engineers to characterize estuarine habitats and processes, including the sediment budget of the Skagit River and the influence of river-delta channelization on sediment transport. Information quantifying the distribution of habitats and extent that sediment transport influences habitats and the morphology of the delta is useful for planning for salmon recovery, agricultural resilience, flood risk protection, and coastal change associated with sea-level rise.