This dataset is a map of in-channel hydrogeomorphic units (HGUs) for an approximately 15 kilometer (km) reach of the Kalamazoo River between the Trowbridge Dam and Allegan, Michigan (MI). HGUs are the building blocks of the riverscape, including, for example, bars, banks, riffles, and pools. The HGUs were mapped with the automated Geomorphic Unit Tool (GUT; Bangen et al., 2017; Wheaton et al., 2015) run on a digital elevation model (DEM) comprising topographic and bathymetric data covering the channel bed, banks, and floodplain for Area 5 of the Kalamazoo River (Quantum Spatial, 2017). The DEM was created from topobathymetric aerial lidar data collected in November, 2016, combined with multibeam bathymetric data collected in May, 2017 to fill gaps in the lidar.