Abstract: Investigation of groundwater variable-density flow and solute transport is usually limited in a 2D system. There are only a few studies performed in a 3D system. However, there are still studies showing differences in free convection between the 2D and 3D systems. This study systematically investigates the variable-density solute transport processes in the 2D and 3D systems through numerical simulations of SEAWAT-2000 and quantifies the system instability, solute spreading and dilution using the Sherwood number, spatial moments and dilution index. The results show that the separate fingers form in the 2D system while they are suppressed in the 3D system due to the enhanced diffusion. However, the instability is stronger and the convective infiltration is faster in the 3D system, which is not directly related to the fingering phenomenon. Furthermore, dilution is stronger in the 3D system, and it reaches to the maximum values at a faster rate in the 2D system. The traditional second central moment may lead to the wrong estimation of spreading and solute dilution in free convection and unstable solute transport. These outcomes help predict properly free convection and solute transport in three-dimensional natural aquifers.