River bathymetry has a crucial role in numerical modelling of flow hydrodynamics. The aim of the present study is to (1) investigate the capability of three different methods to trace the river bed, with the geodetic data derived from in situ survey of the river bed topography to be used as reference data, and moreover (2) assess the impact of the different river geometries on the performance of a one‐dimensional (1D) model of flood hydraulics. The Hydrologic Engineering Center's River Analysis System (HEC‐RAS) hydraulic model, in particular, calibrated and validated on hydrometric data uses a number of cross‐sections derived from aerial laser scanning (ALS), artificial sinking of riverbed, and acoustic Doppler current profiler (ADCP) methods. Water level, discharges, and flood extent derived from the model for 3 N‐year floods (Q1, Q50, Q100) were evaluated while the extent of the inundation areas were exported into geographic information systems for visualisation and interpretation of the findings. Case study area is a 2.2 km river section of the Otava River (Czech Republic), with a history of flood events. The results showed that ALS data need further processing when dealing with the riverbed zone, while ADCP presented high correlation to the reference model.