Considering the fact that a large volume of iron reserve in the Sechahoon Iron Mine in Yazd Province has located under the water table, it is necessary to conduct a comprehensive study on water flow within the pit and its surroundings. The conceptual model of the aquifer was created using surface and underground geological information compared with water table data of the area of interest. In the data preparation stages, in order to create the numerical model, Logan and Lufran tests were studied to determine the hydrodynamic coefficients of the layers, precipitation and evaporation were investigated, and fractures and faults of the region, as a medium for flow channels in the hard formation, were also studied. The model was created in a transient state between 2000 and 2014. To validate its results, the water table was measured 4 times in the last 4 months of 2014. Considering the complexities in the heterogeneous fractured aquifer of the study area, numerical modeling results for the basin in a transient state present 90 percent correlation with field studies. Having investigated the water balance in the region, the boundary condition of the model was determined as the input water from the eastern south and the runoff water in the western north of the region. Since the general trend of faults in the area is north-south, variation in the water table is slight on north-south and intense on the east-west direction. On the other hand, due to the fact that the maximum flow is along the faults and fractures, the water table contour lines in different locations over the region are closed.