One-dimensional hydrodynamic models overestimate river cross-section derived from freely available SRTM DEMs. The present study aims to minimize the overestimation of river flow. DEM-extracted cross-sections obtained from 30 m and 90 m resolutions show higher elevation values than the actual river cross sections of Krishna and Bhima rivers, India. To minimize the overestimation of the river flow, DEM-extracted cross-sections are modified using known cross-section of the river. The corrections for cross sections extracted from DEM, are obtained by subtracting the DEM-derived cross-sections from a known cross-section of the river. Monsoons flows that occurred in years 2006 and 2009 in Krishna and Bhimariver have been used for modeling. The MIKE HYDRO River model performance with modified DEM-extracted cross-sections of river improves as the correlation coefficient, root mean square error, index of agreement, Nash Sutcliffe efficiency & Percentage deviation in peak (%) values are improved.