In porous media, colloids (including nanoparticles, bacteria, and fine particles) are ubiquitous and lie in suspension in a carrier fluid or are attached at interfaces such as the pore walls or the interface between two immiscible fluids (air-water or water-oil for example). The nature of the particles can vary significantly and their presence in the soils and subsurface may be desired or on the contrary, avoided. For example, engineered metal nanoparticles are injected into the subsurface for groundwater remediation. Inversely, the in situ precipitation and subsequent transport of reactive solid particles in far-from-equilibrium conditions or the detachment and mobilization of fines - small particles of sand or clay loosely attached to the pore walls - by hydrodynamics forces threaten geothermal and oil reservoir productivity by reducing permeability near the wells. Other situations of prime interest include the transport of bacteria and viruses, the adsorption of asphaltenes at oil/water interfaces, and the fate of micro-nano plastics. We developed a high-resolution pore-scale simulator to investigate particle depositions and permeability reduction for various flow, pH, and salinity conditions. Our approach relies on a four-way CFD-DEM (Computational Fluid Dynamics - Discrete Element Method) coupling in which fluid flow is governed by Navier-Stokes equations in a fixed grid and the particle dynamics is described in a Lagrangian frame. The model accounts for contact forces as well as long-range interactions including Van der Waals and electrostatic forces. Our model captures the different mechanisms responsible for pore-clogging: sieving, bridging, and aggregation of particles. The numerical model is successfully benchmarked using well-controlled microfluidic experiments.