Rock fractures can serve as water conducting structures for fluid flow and mass transport within the Earth’s crust. Large apertures, which enable high flow velocities, and a rock matrix with several orders of magnitude lower permeability, are accountable that those structures serve as preferential conduits for solutes and colloids. The mechanistic understanding of fundamental transport and retention processes is essential to make reliable predictions of the fate of solutes and colloids in the subsurface. This comprehensive topic is of paramount importance in many areas of geo-engineering, for example disposal of nuclear waste in deep geological formations, enhanced geothermal systems, CO2 sequestration, gas and oil industry, and contaminant transport in groundwater systems. This cumulative Ph.D. thesis deals with the investigation of the impact of flow channel geometry on solute and colloid transport through natural rough fractures. The bottom-up approach used in this thesis helped to investigate separately the mechanisms and the processes on mass transport (solute and colloids) in four steps. All experiments in this thesis were conducted under hydraulic and chemical settings establishing laminar flow and overall unfavorable colloid attachment conditions.