You can use Geo-HMS tool which is compatible with Arc GIS and there you do all the processing for the watershed and generate a project for HEC-HMS. After that you can export the project and do simulate discharge in HEC-HMS using Kinematic wave approach. Attached file would be helpful for you. 

You could also use the distributed hydrological model wflow (HBV or sbm) implemented in the PCRaster Python framework. You can find more info at https://publicwiki.deltares.nl/display/OpenS/Home

You can use Geo-HMS tool which is compatible with Arc GIS and there you do all the processing for the watershed and generate a project for HEC-HMS. After that you can export the project and do simulate discharge in HEC-HMS using Kinematic wave approach. Attached file would be helpful for you. 

I have your same issue and i'm looking papers and articles related to these topics. Thanks to the Geo-plug in provide by HEC i solved easly some problems. I attached the links for user manuals and for download the most usefull tools i found. (I also found interesting tutorials on Youtube)

http://www.hec.usace.army.mil/software/hec-geohms/downloads.aspx

http://proceedings.esri.com/library/userconf/proc98/proceed/TO400/PAP400/P400.HTM

You can use in each GIS pixel an analytically solved  non-linear reservoir equation representing the kinematic wave solution at finite scales as described in:

Liu Z. and Todini E. (2002). Towards a comprehensive physically based rainfall-runoff model. Hydrology and Earth System Sciences, 6(5): 859–881.

Liu Z. and Todini E. (2004) - Assessing the TOPKAPI non-linear reservoir cascade approximation by means of a characteristic lines solution, Hydrological Processes, 19(10): 1983–2006.

Reggiani, P., Todini, E. and Meißner, D., (2014) – Analytical solution of a kinematic wave approximation for channel routing, Hydrology Research, 45.1: 43-57. 

For estimating discharge using GIS or Arc Hydro is scientifically not possible unless you use fully integrated and spatially distributed hydrological model like MIKE SHE (professional) or MIKE SHE (enterprise) to include all hydrological processes, e.g., surface/subsurface flow, river and drains flow, crops and vegetation layer integrated in it using at least 50x50m DEM. 

Hi Ajay,

Many hydrological models can be used for estmating discharge using GIS. The WEPP model can be used for watershed discretisation and you can use KINEROS model, ANSWERS model, CATHY model and others. 

Thanks all, I am aware of using hydrological models to simulate the discharge but solving the problem using GIS alone seems not be practical. 

You could have a look at my manuscript to found on research gate. This has proved high applicabilty and efficiency over decades

https://www.researchgate.net/publication/264225677_A_generic_mathematical_formulation_of_a_piecewise_linear_approximation_of_non_linear_hydrological_storage_processes

Article A generic mathematical formulation of a piecewise linear app...