I personally believe that one of the best software for modeling different structures in rivers and canals is ISIS or FloodModeler that firstly developed by Wallingford company. In the following link you can download this Package:
RFEM allows for design and analysis of very complex structures containing many surfaces and solids. Therefore, it is perfectly suited for static and dynamic analysis of hydraulic steelworks like sluices, locks and lock chambers, water gates such as roller, sliding and sector gates, weir flaps, drum gates, flood protection gates, ship lifts, canal bridges, and many others.
I find FHWA Hydraulic Toolbox 4.2 very usefully in the analysis of channels, weirs, gutters and inlets, detention basins, and particle gradations. The Hydraulic Toolbox also includes Rational Method hydrologic analysis tools.
Also very interesting is the HEC-RAS 5.2 (1D or 2D or both) of Hydrologic Engineering Center's (CEIWR-HEC) River Analysis System (HEC-RAS). This software allows the user to perform one-dimensional steady flow, one and two-dimensional unsteady flow calculations, sediment transport/mobile bed computations, and water temperature/water quality modeling
Check on http://www.hec.usace.army.mil/software/hec-ras/