As groundwater is an essential nutrition and irrigation resource, its pollution may lead to catastrophic consequences. Therefore, accurate modeling of the pollution of the soil and groundwater aquifer is highly important. As a model, we consider a density-driven groundwater flow problem with uncertain porosity and permeability. This problem may arise in geothermal reservoir simulation, natural saline-disposal basins, modeling of contaminant plumes, and subsurface flow. This strongly nonlinear time-dependent problem describes the convection of the two-phase flow. This liquid streams under the gravity force, building so-called "fingers". The accurate numerical solution requires fine spatial resolution with an unstructured mesh and, therefore, high computational resources. Consequently, we run the parallelized simulation toolbox ug4 with the geometric multigrid solver on Shaheen II supercomputer. The parallelization is done in physical and stochastic spaces. Additionally, we demonstrate how the ug4 toolbox can be run in a black-box fashion for testing different scenarios in the density-driven flow. As a benchmark, we solve the Elder-like problem in a 3D domain. For approximations in the stochastic space, we use the generalized polynomial chaos expansion. We compute the mean, variance, and exceedance probabilities of the mass fraction. As a reference solution, we use the solution, obtained from the quasi-Monte Carlo method.This work is a 3D extension of our previous 2D work [47]. The problem setup is the same; the difference is only in the aquifer. In this work, we consider two 3D aquifers. These new 3D geometries contain a much larger number of degrees of freedom (DoFs), and, therefore, numerical experiments require significantly more computational resources.Accurate prediction of the contamination of the groundwater is highly essential. Certain pollutants are soluble in water and can leak into groundwater systems, such as seawater into coastal aquifers or wastewater leaks. Indeed, some pollutants can change the density of a fluid and induce density-driven flows within the aquifer. This causes faster propagation of the contamination due to convection. Thus, simulation and analysis of this density-driven flow play an important role in predicting how pollution can migrate through an aquifer [28,43].In contrast to the transport of pollution by molecular diffusion, convection due to density-driven flow is an unstable process that can undergo quite complicated patterns of distribution. The Elder problem is a simplified but comprehensive model that describes the intrusion of salt water from a top boundary into an aquifer [23,24, 25,79]. The evolution of the concentration profile is typically referred to as fingering. Note that due to the nonlinear nature of the model, the distribution of the contamination strongly depends on the model parameters, so that the system may have several stationary solutions [40].