The Horizontal Reactive Media Treatment well (HRX well) is a horizontal well laid along the direction of groundwater flow and filled with a reactive media. It is a novel technology for in-situ treatment of contaminated groundwater. The HRX well passively captures groundwater flow through the higher in-well hydraulic conductivity relative to the aquifer hydraulic conductivity. The most significant technical performance risk associated with field-scale implementation of the HRX well is installation and construction. Therefore, the groundwater capture simulation plays a very important role in the design of HRX well.We propose a cell-based smoothed radial point interpolation method (CS-RPIM) for simulating groundwater flow captured by HRX well in a 3D test pit. This numerical formulation is based on tetrahedral background meshes which can be generated automatically. The cell-based local smoothing domain makes CS-RPIM an ideal way for simulating groundwater flow in the environment with multiple hydraulic conductivities. The generalized smoothed Galerkin weak form makes it possible to select local support nodes more flexibly than the standard weak form. The use of multiquadric (MQ) radial basis in creating RPIM shape functions ensures the non-singularity of moment matrix. This method is compared with finite element method (FEM) on the same meshes. Numerical experiments show CS-RPIM has higher accuracy and convergence rate than FEM. We also analysis the effect of the in-well hydraulic conductivity and the dimension of well on the groundwater capture zone.