Dear Dr Muhammad Awais, I would suggest you start by being sure you have a proper conceptual model of the flow domain; the hydraulic parameters need to be defined with a numerical model. It is expected that the flow model is in agreement with chemistry and isotopes distribution as well as with surface indicators of groundwater flow conditions (recharge/discharge). Be sure the correct boundary conditions are considered. If you do so, by the time you run a flow model there will be little adjustments in need. I sincerely hope the following reference might be of some assistance. Do get from Mexico,saludos,jjoel carrillor
Carrillo-Rivera, JJ. S. Ouysse y GJ Hernández-Garcia. 2013. Integrative Approach for Studying Water Sources and Their Vulnerability to Climate Change in Semi-Arid Regions: Drâa Basin, Morocco. International Journal of Water Resources and Arid Environments 3(1): 26-36, 2013 ISSN 2079-7079.