Three-dimensional mathematical models of regional groundwater flow are beneficial to the management of groundwater resources as they allow the approximation of the components of hydrological processes and provide a mechanistic description of the flow of water in an aquifer. Such a modeling study was carried out in Rupen Basin, North Gujarat, India. The study area is characterized by alluvium aquifer system with very heavy abstraction of groundwater for agricultural purposes. The model simulates groundwater flow over an area of about 4706 square kilometers with 74rows, 127 columns, with single vertical layer on the regional model. The detailed study area is divided into rows and columns with a size of 1.0 sq.km grids (Figure.1). The model was simulated in steady and transient state condition using the finite-difference approximation of three-dimensional partial differential equation of groundwater flow in this aquifer from May 2007 to November 2010. The model was calibrated for steady and transient state conditions. There was a reasonable match between the computed and observed heads. Based on the modelling results, the aquifer parameters of this aquifer system is established.