In contrast to dramatic flow regime changes by less frequent large-scale volcanic eruptions, those caused by more frequent small-scale processes in volcanic landscapes may also drastically change the direction and dynamics of flow in a drainage system formed solely by fluvial processes. During such periods of channel morphology change, it is necessary to frequently update channel flow parameters to assess preventive measures for civil protection purposes. Often aerial photography is impracticable, since parts of the channels are covered by dense vegetation, while total station and laser topographic surveys are often too slow and costly, particularly during a high frequency of events. This article introduces and validates a new methodology for updating the representation of channel morphology in Digital Elevation Models (DEM) used specifically for assessing the dangers of frequently occurring lahars along gorges in volcanic landscapes during eruptive and non-eruptive periods. The updating of channel cross-sections was achieved by inserting more detailed representative profiles of homogeneous channel sectors in DEMs derived from existing less detailed topographic maps. The channel profiles were surveyed along the thalweg in equidistant points according to Universal Transverse Mercator (UTM) (x,y) coordinates and elevation derived from the existing DEM. The proposed technique was applied at Tenenepanco-Huiloac Gorge on Popocatépetl volcano, Mexico, in an area affected by major lahars during the volcano’s most recent eruptive period from 1994 to 2005. The proposed method can reduce the cost and person-hours of a regular channel topographic survey dramatically and the enhanced DEM can determine volume parameters and flood zones associated with the 1 July 1997 and 21 January 2001 lahars, respectively. In addition, the updated DEM with better channel representation allowed a more realistic fluid flow and lahar simulation with the process-based TITAN2D model.