Most flood inundation models do not come with an uncertainty analysis component chiefly because of the complexity associated with model calibration. Additionally, the fact that the models are both data-and compute-intensive, and since uncertainty results from multiple sources, adds another layer of complexity for model use. In the present study, flood inundation modeling was performed in the Godavari River Basin using the Hydrologic Engineering Center—River Analysis System 2D (HEC-RAS 2D) model. The model simulations were generated for six different scenarios that resulted from combinations of different geometric, hydraulic and hydrologic conditions. Thus, the resulted simulations account for multiple sources of uncertainty. The SRTM-30 m and MERIT90 m Digital elevation Model (DEM), two sets of Manning’s roughness coefficient (Manning’s n) and observed and estimated boundary conditions, were used to reflect geometric, hydraulic and hydrologic uncertainties, respectively. The HEC-RAS 2D model ran in an unsteady state mode for the abovementioned six scenarios for the selected three flood events that were observed in three different years, i.e., 1986, 2005 and 2015. The water surface elevation (H) was compared in all scenarios as well as with the observed values at selected locations. In addition, ‘H’ values were analyzed for two different structures of the computational model. The average correlation coefficient (r) between the observed and simulated H values is greater than 0.85, and the highest r, i.e., 0.95, was observed for the combination of MERIT-90 m DEM and optimized (obtained via trial and error) Manning’s n. The analysis shows uncertainty in the river geometry information, and the results highlight the varying role of geometric, hydraulic and hydrologic conditions in the water surface elevation estimates. In addition to the role of the abovementioned, the study recommends a systematic model calibration and river junction modeling to understand the hydrodynamics upstream and downstream of the junction. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.