Installation of a partially penetrating well (PPW) in which only a portion of the well casing is screened is becoming more common because it is very often the case that only a portion of the vertical thickness of the aquifer is contaminated. In this study, we present a mathematical model describing the contaminant transport towards a PPW. To construct the model, the radial and vertical components of the pore water velocity are first computed using an analytical solution for the steady-state drawdown distribution near a PPW. Next, the obtained radial and vertical components of the pore water velocity are incorporated into a three-dimensional axially symmetrical advection-dispersion equation in cylindrical coordinates from which the solute transport equation is derived. The Laplace transformed finite difference technique is then adopted to solve the governing equation. The case that contaminant plume is distributed only over the lowermost 20% vertical thickness of the aquifer is considered for simulation. Breakthrough curves at the extraction well and the total mass removal of the contaminant by pumping are both obtained to illustrate how the aquifer remediation using a PPW is affected by various site-specific hydrogeological parameters. Results demonstrate that the use of the PPW can effectively remove the contaminant only for the aquifer that has a large hydraulic conductivity anisotropy ratio and a small longitudinal dispersivity. The fully penetrating well performs equally or better than the PPW for an aquifer with large longitudinal dispersivity. Moreover, the temporal evolution of the contaminant plume is depicted to gain further insight into the contaminant transport towards a PPW affected by various hydrogeological parameters. The mathematical model presented herein provides a useful tool for designing an effective and efficient pump-and-treat system using a PPW. Copyright (C) 2010 John Wiley & Sons, Ltd.