Lesser pathogen prevalence is well recognized in granular versus fractured aquifers; however, the impact of residence time (inactivation/death) versus removal (pore-scale delivery to surfaces) on pathogen prevalence remains unaddressed. The objective of this study was to examine the specific role of pore-scale delivery to surfaces (removal) as an explanation of contrasting pathogen prevalence in granular versus fractured media from Wisconsin. Inactivation/death was obviated by the use of nonbiological colloids in column transport experiments conducted in representative media from the two Wisconsin sites. Trends in retention as a function of colloid size were examined using nano- to microsized (0.1-4.2 μm) carboxylate-modified polystyrene latex microspheres that represented virus- to protozoa-sized pathogens. Several orders of magnitude greater removal of all colloid sizes were observed in granular relative to those in fractured media, whereas the size corresponding to minimum retention contrasted between the two media. Particle trajectory simulations in collectors (flow fields with surfaces) representing granular versus fractured media captured the observed contrasting retention and trends with colloid size. These results demonstrate that flow impingement on surfaces at forward flow stagnation zones drives contrasting pore-scale delivery to surfaces in granular versus fractured media and potentially the observed contrasting pathogen prevalence in granular versus fractured aquifers.