Fine‐scale alterations found on fracture surfaces and between fracture surfaces and rock matrix are key uncertainties that need to be considered when developing solute transport models for fractured crystalline rocks. This paper presents a comprehensive approach developed for coupling laboratory tests, microscopic observations, and modeling in order to understand and quantify tracer transport processes occurring in natural fracture surfaces, using a single‐fractured granodiorite sample from the Grimsel Test Site, Switzerland. Laboratory tests including through‐diffusion, batch sorption, and flow‐through tests using five tracers with different retention properties indicated that tracer retention was consistently in the sequence of HDO or HTO (deuterated or tritiated water) ≈ Se < Cs < Ni < Eu and as well as showing the existence of a diffusion‐resistance layer near the fracture surface, cation excess, and anion exclusion effects for diffusion. Microscale heterogeneities around the fracture were clarified and quantified by coupling X‐ray computed tomography and electron probe microanalysis. A three‐layer model incorporating as much data as possible including weathered vermiculite, foliated mica, and undisturbed matrix layers, and their properties such as porosity, sorption, and diffusion parameters, obtained from laboratory diffusion tests and microscopic observations, provided a much better interpretation for breakthrough curves and concentration distributions near‐fracture surface of all tracers, measured in flow‐through tests, than either a one‐ or two‐layer model. Mechanistic understanding and detailed modeling considering the effects of fine‐scale surface alteration around a natural fracture should improve confidence for the safety assessment in fractured crystalline rocks.