A reach-scale high resolution digital elevation model (DEM) of the Congo’s main stem bathymetry is presented. The Bathymetry DEM covers a multichannel reach of the main stem situated in the Cuvette Centrale, and is developed from a series of in-situ measurements of bathymetry, water surface elevation and discharge that were obtained during a CRuHM fieldtrip in summer 2017. The main stem’s complex network of channel threads requires a bathymetry modelling methodology that is capable of intelligently interpolating the raw bathymetry measurements. The methodology must also estimate a significant portion of the bathymetry, since it is not feasible to measure the entire extent of the massive and complex channel network that this study reach is comprised of. This methodology is also presented. Remote sensing from satellites is increasingly being used to resolve the scarcity of contemporary hydrological and hydrographic measurements in the Congo Basin. However, river channel bathymetry information cannot yet be reliably obtained from remote sensing methods. This is problematic since river channel representation has been shown to be an essential input into a hydraulic model. Analyses of satellite observations suggest that, relative to other global rivers, in-channel flows on the Congo’s main stem represent a relatively large proportion of total flows through the river-floodplain system. This implies the Congo’s in-channel bathymetry may play a relatively large role in controlling Congo main stem hydrodynamics. When used in a hydraulic model, the bathymetry DEM presented here will provide new information on Congo in-channel hydraulics and the extent to which bathymetry controls the Congo’s middle reach hydrodynamics. It will help better quantify the capacity of the Congo main stem channels through the Cuvette Centrale, and thus provide further insights into the extent to which the main stem channel floods in this region. It is also intended to be used for testing simplified methods of Congo bathymetry representation that are necessary for larger scale hydraulic models.