Colloids, which range in size from nanometres to micrometres, can deposit within pore spaces, clogging flow pathways and significantly altering permeability. While the porosity reduction and clogging effects caused by micron-sized particles have been studied extensively, the dynamic effects of nanoparticles on permeability reduction and flow redistribution in three-dimensional porous media remain largely unresolved. To address this gap, I conduct time-resolved 3D X-ray micro computed tomography (micro-CT) to visualize nanoparticle (NP) transport, retention, and clogging processes in situ. Our innovative experiments can effectively track how nanoscale colloid deposition modifies hydrodynamic conditions within complex pore networks, thereby uncovering mechanisms that have often been overlooked in traditional 2D microfluidics or bulk column studies. These groundbreaking experiments delivered the first direct visualization of nanoparticle transport and clogging phenomena in 3D porous media over time, revealing how deposition initiates and propagates throughout intricate pore networks while altering local hydrodynamics. This process drives significant permeability reduction along with notable flow redistribution patterns. The findings have strong implications for developing improved predictive models for colloid transport dynamics as well as groundwater remediation strategies, contaminant migration assessments, and subsurface energy storage applications.