HEC-RAS allows you to perform one-dimensional steady flow, unsteady flow, sediment transport/mobile bed computations, and water temperature modeling. http://www.hec.usace.army.mil/software/hec-ras/

Hydrologic Modeling System (HEC-HMS) is designed to simulate the precipitation-runoff processes of dendritic watershed systems.

http://www.hec.usace.army.mil/software/hec-hms/
 

EPANET is software that models water distribution piping systems. EPANET is public domain software that may be freely copied and distributed. It is a Windows 95/98/NT/XP program. EPANET performs extended period simulation of the water movement and quality behavior within pressurized pipe networks.

http://www.epa.gov/nrmrl/wswrd/dw/epanet.html