Charged porous media are pervasive, and modeling such systems is mathematically and computationally challenging due to the highly coupled hydrodynamic and electrochemical interactions caused by the presence of charged solid surfaces, ions in the fluid, and chemical reactions between the ions in the fluid and the solid surface. In addition to the microscopic physics, applied external potentials, such as hydrodynamic, electrical, and chemical potential gradients, control the macroscopic dynamics of the system. This paper aims to give fresh overview of modeling pore-scale and Darcy-scale coupled processes for different applications. At the microscale, fundamental microscopic concepts and corresponding mass and momentum balance equations for charged porous media are presented. Given the highly coupled nonlinear physiochemical processes in charged porous media as well as the huge discrepancy in length scales of these physiochemical phenomena versus the application, numerical simulation of these processes at the Darcy scale is even more challenging than the direct pore-scale simulation of multiphase flow in porous media. Thus, upscaling the microscopic processes up to the Darcy scale is essential and highly required for large-scale applications. Hence, we provide and discuss Darcy-scale porous medium theories obtained using the hybrid mixture theory and homogenization along with their corresponding assumptions. Then, application of these theoretical developments in clays, batteries, enhanced oil recovery, and biological systems is discussed.