Saltwater, or brine, underlies freshwater in many aquifers, with a transition zone separating them. Pumping freshwater by a well located above the transition zone produces upconing of the latter, eventually salinizing the pumped water, forcing shut-off. Following the well’s shut-off, the upconed saltwater mound undergoes decay, tending to return to the pre-pumping regime. The FEAS code is used for the simulation of coupled density-dependent flow and salt transport involved in the upconing–decay process. In this code, the flow equation is solved by the Galerkin finite element method (FEM), while the advective–dispersive salt transport equation is solved in the Eulerian–Lagrangian framework. The code does not suffer from the instability constraint on the Peclet number. The code is used to investigate the transient upconing–decay process in an axially symmetric system and to discover how the process is affected by two major factors: the density difference factor (DDF) and the dispersivities. Simulation results show that under certain conditions, pumping essentially freshwater can be maintained for a certain time period, the length of which depends on the dispersivity values used. A recirculating flow cell may occur in the saltwater layer beneath the pumping well, widening the saltwater mound. The decay process is lengthy; it takes a long time for the upconed saltwater to migrate back to its original shape of a horizontal transition zone prior to pumping. However, the wider transition zone caused by hydrodynamic dispersion can never return to the initial one. This indicates that once a pumping well is abandoned because of high salinity, it can be reused for groundwater utilization only after a long time. It is also shown that the upconing–decay process is very sensitive to DDF, which, in our work, ranges from 0 (for an ideal tracer) to 0.2 (for brine). For a DDF of 0.025 (for seawater), local upconing occurs only for low iso-salinity surfaces, while those of high salt concentration remain stable after a short time. For an ideal tracer, all iso-salinity surfaces rise toward the pumping well, whereas for brine only iso-salinity surfaces of very low salinity upcone towards the pumping well. This may imply that the traditional finding that the sharp interface approximation is practically close to the 0.5 iso-salinity surface may not be true for a high DDF solution.