Most of the groundwater simulation models are based on certain element (finite element method) or grid (finite difference method) formulation which is used for obtaining the transient head variation in the aquifer system. Since groundwater management scenarios often demand to call these simulation models several hundred times to deliver the acceptable decision variables, it is essential that an efficient and accurate system simulation technique should be adopted. In this paper, a recently developed global collocation approach based meshfree (Mfree) model is used as a groundwater state estimation tool. The developed model is first tested on a twodimensional confined aquifer synthetic flow problem where the results are compared with the available analytical and numerical solutions. Different time steps and varied pumping schedules were also assessed for a performance check. Later the tested model is applied to a synthetic aquifer flow problem having a close analogy to real field variability. The results obtained through the projected Mfree model are the testimony of accuracy and successful application of the developed model.