Colloidal transport and clogging in porous media is a phenomenon of critical importance in many branches of applied sciences and engineering. It involves multiple types of interactions that span from the sub-colloid scale (electrochemical interactions) up to the pore-scale (bridging), thus challenging the development of representative modelling. So far published simulation results of colloidal or particulate transport are based on either reduced set of forces or spatial dimensions. Here we present an approach enabling to overcome both computational and physical limitations posed by a problem of 3D colloidal transport in porous media. An adaptive octree mesh is introduced to a coupled CFD and DEM method while enabling tracking of individual colloids. Flow fields are calculated at a coarser scale throughout the domain, and at fine-scale around colloids. The approach accounts for all major interactions in such a system: elastic, electrostatic, and hydrodynamic forces acting between colloids, as well as colloids and the collector surface. The method is demonstrated for a single throat model made of four spherical segments, and the impact of clogging is reported in terms of the evolution of the critical path diameter for percolation and permeability. We identified four stages of clogging development depending on position and time of individual colloid entrapment, which in turn correlates to a cluster evolution and local transport.