The interaction of monodisperse fluorescent carboxylated polystyrene colloids (25 nm and 1000 nm diameter) with a cut granodiorite surface (Grimsel granodiorite; Switzerland) and with acrylic glass is investigated both experimentally and numerically. Colloid transport experiments are conducted in a parallel plate type fracture flow cell with an aperture of 0.75 mm at pH 5 under low ionic strength (1 mM NaCl) and under laminar flow (7 mL/h) conditions. The study focuses on the effect of residence time, colloid size, collector material and fracture orientation on colloid retention. Long colloid residence times are achieved by stop-flow experiments. Using atomic force microscopy and, more specifically, the colloid probe technique surface roughness and force distance information of the collector material (granodiorite or acrylic glass) as a function of probe size (cantilever) are obtained. The experiments are modeled using COMSOL Multiphysics (R) (2-D numerical simulations). The experimental and the modeled results lead to the conclusion that large colloids (1000 nm diameter) undergo sedimentation and deposition on the surface during stop-flow. Collector interaction is not affected by the surface roughness variation. Contrariwise, for the investigated 25 nm colloids sedimentation does not play a role under the experimental conditions and collector interaction is triggered by surface inhomogeneities such as surface roughness. (C) 2016 Elsevier Inc. All rights reserved.