In this paper we quantify the influence of geometry and distribution of surface roughness to the directional anisotropy of fluid flow and transport properties of a single fracture. Roughness of fractures appears to have first order control on how they behave mechanically and hydraulically. We directly quantified the surface roughness of a single fracture using high-resolution laser scanning confocal microscopy. This roughness was input into directly coupled numerical models of fluid flow and transport. We simulated the transport of colloids (microspheres) through the fracture. We found tailing in the breakthrough and sensitivity of the breakthrough to flow direction in the fracture. Microspheres were observed to be trapped in low velocity zones on the lee side of fracture walls. This was not observed in smooth or sinusoidal varying fracture wall geometries. These observations have significant implications for quantifying the transport of dissolved and solid phase materials (colloids) through fractured rock.