Abstract: Numerical simulations are an important tool for quantitative research on the volume and quality of groundwater. To reveal the cause of an abnormal waterhead phenomenon using the finite element method, a three-dimensional inhomogeneous model is applied as a case study. The Lumped Mass method is an alternative approach for computing storage changes, which can be used to ameliorate abnormal waterheads. In this paper, the Lumped Mass method is applied to an abnormal waterhead phenomenon by analyzing the local conservation. It is observed that the advection fluxes in the control domain of a vertex refer to the hydraulic gradients in that slice and in adjacent slices. As water starts to be pumped, the potential of the well vertex decreases rapidly. This leads to a positive flux flowing into the control domain of an adjacent vertex in an adjacent slice. The storage change of the control domain in this adjacent vertex is positive, and so the potential increases. Hence, the computation of advection fluxes in the finite element method is the cause of the abnormal waterhead phenomenon.