Boundary conditions are required to close the mathematical formulation of unstable density-dependent flow systems. Proper implementation of boundary conditions, for both flow and transport equations, in numerical simulation are critical. In this paper, numerical simulations using the FEFLOW model are employed to study the influence of the different boundary conditions for unstable density-dependent flow systems. A similar set up to the Elder problem is studied. It is well known that the numerical simulation results of the standard Elder problem are strongly dependent on spatial discretization. This work shows that for the cases where a solute mass flux boundary condition is employed instead of a specified concentration boundary condition at the solute source, the numerical simulation results do not vary between different convective solution modes (i.e., plume configurations) due to the spatial discretization. Also, the influence of various boundary condition types for nonsource boundaries was studied. It is shown that in addition to other factors such as spatial and temporal discretization, the forms of the solute transport equation such as divergent and convective forms as well as the type of boundary condition employed in the nonsource boundary conditions influence the convective solution mode in coarser meshes. On basis of the numerical experiments performed here, higher sensitivities regarding the numerical solution stability are observed for the Adams-Bashford/Backward Trapezoidal time integration approach in comparison to the Euler-Backward/Euler-Forward time marching approach. The results of this study emphasize the significant consequences of boundary condition choice in the numerical modeling of unstable density-dependent flow.