Bathymetric and topographic data on the mainstem Nooksack River, Whatcom County, Washington were collected in the fall of 2015 as part of a study on sediment transport and channel change. Bathymetric data was collected from the river's mouth to river mile (RM) 28, near Nugent's Corner. Topographic data is available from RM 17, near the town of Lynden, to RM 37, near the confluence of the Middle Fork Nooksack. More information on these datasets is available in their respective metadata. The overlapping extents of these surveys were merged to create a seamless elevation data set of the river bed and active channel. Aerial lidar acquired in 2013 was used to fill in holes where vegetation prevented photogrammetric reconstructions and to provide elevation data for the floodplain.