Modeling flow and transport in porous media requires the management of complexities related both to physical processes and to subsurface heterogeneity. A thorough approach needs a great number of spatially-distributed phenomenological parameters, which are seldom measured in the field. For instance, modeling a phreatic aquifer under high water extraction rates is very challenging, because it requires the simulation of variably-saturated flow. 3D steady groundwater flow is modeled with YAGMod (yet another groundwater flow model), a model based on a finite-difference conservative scheme and implemented in a computer code developed in Fortran90. YAGMod simulates also the presence of partially-saturated or dry cells. The proposed algorithm and other alternative methods developed to manage dry cells in the case of depleted aquifers are analyzed and compared to a simple test. Different approaches yield different solutions, among which, it is not possible to select the best one on the basis of physical arguments. A possible advantage of YAGMod is that no additional non-physical parameter is needed to overcome the numerical difficulties arising to handle drained cells. YAGMod also includes a module that allows one to identify the conductivity field for a phreatic aquifer by solving an inverse problem with the comparison model method.