Nowadays, because of high adaptability for advanced simulation models for groundwater, these models are comprehensively applied in management and exploitation of groundwater resources. The aim of this study was toinvestigate and simulate the groundwater resources in Kouhpayeh-Segzi watershed and in particular estimation the hydrodynamic coefficients of unconfined aquifer in sub-basin. After preparation of input layers for model, efficient parameters in modeling, boundary conditions and aquifer gridding were determined. Then, based on the available data, model was run and calibrated in a steady state for water year 2002 and in a transient state for water years between 2002 and 2004. The simulation outputs were confidently verified for water year 2005.The results indicated that the hydraulic conductivities and storage coefficients were ranged on the different regions on sub-basin from 15.26 to 19.87 m/day and 0.0107 to 0.0186, respectively. From aquifer's hydrograph for a period from 1995 to 2012, water level was slightly declined about 25 cm. This may be due to two regions where are covered by an irrigation network (green area). It's caused that water level raised. By ignoring of these recharge areas, water level was declined up to 80 cm per year. The sensitivity analysis in transient state was verified the results of model calibration. In addition, the hydraulic head values computed by MODFLOW were well agreed with those that were collected from all piezometers. Keywords : Modeling, MODFLOW, Kouhpayeh-Segzi, Groundwater, Hydrodynamic coefficients.