The need to reduce the computational cost of stochastic groundwater flow and mass transport predictions calls for efficient upscaling techniques which can transfer the heterogeneity across scales while preserving similar flow and transport behaviors. In addition, due to the scarcity of measurement data, inverse modeling is commonly used to calibrate the parameters by conditioning on direct and indirect data and hence reduce the uncertainty of flow and transport predictions. In this work, an upscaling technique is developed and applied both in a synthetic example and a real case; then upscaling and the Ensemble Kalman Filter (EnKF, a method for inverse modeling) are coupled to handle a high-resolution inverse model; and finally, the EnKF and its variant, the normal-score EnKF, is applied in the context of multiGaussian and nonmultiGaussian media. The work included in this PhD can be grouped in three blocks.First, simple averaging, simple-Laplacian, Laplacian-with-skin, and nonuniform coarsening upscaling techniques are reviewed and assessed in a threedimensional hydraulic conductivity upscaling exercise. The reference is a fine scale conditional realization of the hydraulic conductivities at the MAcroDispersion Experiment site on Columbus Air Force Base in Mississippi (USA). This realization was generated using a hole-effect variogram model and it was shown that flow and transport modeling in this realization (at the fine scale) can reproduce the observed non-Fickian spreading of the tritium plume. The purpose of this work is twofold, first to compare the effectiveness of different upscaling techniques in yielding upscaled models able to reproduce the observed transport behavior, and second to demonstrate and analyze the conditions under which flow upscaling can provide a coarse model in which the standard advection-dispersion equation can be used to model transport in seemingly non-Fickian scenarios. Specifically, the use of the Laplacian-based upscaling technique coupled with a non-uniform coarsening scheme yields the best results both in terms of flow and transport reproduction, for this case study in which the coarse blocks are smaller than the correlation ranges of the fine scale conductivities. However, in some cases, we also observe the impossibility of reproducing transport at the coarse scale solely on the basis of a flow upscaling. For this reason, a methodology for transport upscaling is developed v vi for three-dimensional highly heterogeneous formations. The overall approach requires a prior hydraulic conductivity upscaling using an interblock-centered full-tensor Laplacian-with-skin method followed by transport upscaling. The coarse scale transport equation includes a multi-rate mass transfer term to compensate for the loss of heterogeneity inherent to all upscaling processes. The upscaling procedures for flow and transport are described in detail and then applied to a three-dimensional highly heterogeneous synthetic example. The proposed approach not only reproduces flow and transport at th...