Hydrodynamic and sediment transport models are useful engineering tools for predicting flood flow. Many models such as HEC-RAS, HEC-6, IALLUVIAL, SRH-1D were developed for perennial rivers, and may not be suitable to ephemeral rivers in arid and semi-arid regions. This paper outlines a comparison study that examined the water surface and bed elevations of a flood event exceeding 100-year flood in the Rillito River at Tucson, Arizona. The result of IALLUVIAL2, HEC-RAS and GSTAR1D models were compared with field survey data. Results showed that IALLUVIAL2, which cannot compute bridge effects, predicted a flood similar to that of the more commonly used HEC-RAS model, which take bridges into account. Both models underestimated the flooding by about 2 to 4 feet, but accurately predicted the progression of each flood flow. This study also found the most appropriate sediment transport and roughness equations for this particular river are Laursen sediment equation and Manning's relation. The results indicated the need of an appropriate model for predicting flood flows in ephemeral streams for water resource managers, engineers, and urban planners.