Transport of colloids in fractured media has gained a considerable importance in recent years, mainly in the field of chemical pollutant transport and in nuclear waste management in groundwater system. The major reason being, colloids assist in migration of radionuclides through fractured rocks. Field studies and experiments have shown that natural fractures have apertures which are complex in geometry and vary spatially. An attempt has been made to numerical model the colloidal transport in a single fracture-matrix system to investigate the mobility of colloids in the presence of variable fracture apertures. To capture the effect of variation of fracture aperture, two different geometrical distributions logarithmic and sinusoidal, have been developed to generate the variations of fracture aperture. Analysis for both linear and nonlinear sorption isotherm cases has been carried out. The nonlinear sorption isotherm has been carried out given by Langmuir and Freundlich of isotherms. Cauchy type of boundary condition is applied at the fracture inlet to better represent the field scenario. The results indicate that colloidal migration in fracture and rock matrix is sensitive to fracture aperture variation and the parallel plate model exaggerates the colloid concentration in fracture. Further the results also suggest that the type of colloid source condition has a profound effect on the migration of the colloids in fracture and rock matrix. © 2014, Capital Publishing Company.