The main problem presented in this paper is the safety inlet navigation of the waterway below the bridge in the city of Kaunas in Lithuania. The analyzed reach is located in the Nemunas river downstream of the Kaunas dam. It is a part of the waterway E–41 leading to the Klaipeda harbor on the southern coast of the Baltic Sea. The work was initiated by the Lithuanian company UAB “Inžinerinis projektavimas” with funds from the project called European Union Trans-European Transport Network (EU TEN-T) . The main requirement imposed along this reach is to keep sufficient depth even in the range of the lowest flows. The depth is sufficient if it is not lower than 1.15 m for minimum flows such as Q95% and Q95% with ice. The hydraulic conditions for maximum flow Q50%, Q5%, and Q1% are also taken into account for control because the threat of hydraulic jump generation was also noticed. The research is based on georeferenced data from public and non-public sources. The hydrologic data were received from the Lithuanian Hydrometeorological Service. The physical model was created in the Water Laboratory of the Department of Hydraulic and Sanitary Engineering at Poznan University of Life Sciences, Poland. The preprocessing of spatial data in ArcGIS 10.8.2 and rules of hydraulic similarity were implemented in the process of physical model preparation. Three experiments were conducted in the laboratory with scaled values of Q95%, Q5%, and Q1%. The measurements of the water surface and evaluations of the average velocity were used to validate the 2D numerical model prepared in HEC-RAS 6.3.1. The basic layers of the HEC-RAS model were preprocessed in ArcGIS 10.8.2 by ESRI company. The numerical model was implemented to test different values of unknown roughness of the channel bottom. The simulations were conducted for the real values of Q95% and Q95% with ice and Q50%. The results of the simulations were depth and Froude number maps. These maps were classified into zones of no risk, middle risk, and high risk. ArcGIS in the post-processing phase was applied to identify the locations of the hazards. The magnitude of risk was expressed in terms of minimum depth achieved, maximum Froude number, as well as the length of the reaches with high risk related to these two factors. The threat of hydraulic jump formation below the bridge was also noticed. Conducted results confirmed that the combination of hydrodynamic simulations and geoprocessing in the pre- and post-processing stages could be a powerful tool in hydraulic engineering analyses. Additionally, it is worth noting that numerical modeling enables a wider analysis of potential conditions than could be possible with a physical model only.