HEC-RAS

River hydraulics modeling software from the US Army Corps of Engineers

Free Geospatial
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Users build a terrain model, define channels and structures, and simulate steady or unsteady flow. Results include water surface profiles, inundation maps, and sediment transport. It works with GIS data.

The interface is technical and expects hydraulic knowledge.

MIKE and TUFLOW are commercial alternatives. HEC-RAS suits hydrologists and civil engineers.