The transport of 3H+ (as HTO) and 36Cl− (as Na36Cl) was investigated in the dynamic system, i.e., in the columns filled with crushed pure granite and fracture infill of various grain sizes. The aim of column experiments was to determine important transport parameter, such as the retardation, respectively distribution coefficients, Peclet numbers and hydrodynamic dispersion coefficients. Furthermore, the research was focused to quantification of the effect of grain size on migration of studied radionuclides. The experimental breakthrough curves were fitted by a model based on the erfc-function, assuming a linear reversible equilibrium sorption/desorption isotherm, and the above mentioned transport parameters were determined. The results showed that influence of grain size on sorption of 3H+ and 36Cl− was negligible. Retardation and distribution coefficients of both tracers converged to one and zero, respectively, in case of all fractions of crushed granite and infill material. Generally, the presumed ion exclusion of 36Cl in anionic form was proved under given conditions, only very weak one seems to exist in a case of infill material. In principal, both radionuclides behaved as non-sorbing, conservative tracers. On the other hand, the influence of grain size on Peclet numbers value and on dispersion coefficient was observed for both crystalline materials, namely in agreement with theoretical suppositions that the values of Peclet numbers decrease with increasing grain size and values of dispersion coefficient increase.