In this paper, numerical simulations are used to analyze complex flow behavior in partially saturated fractured low-permeability soils during groundwater recharge. The aim is to develop an understanding of the influence of fracture-matrix interactions and different physical parameters on flow processes. A three-dimensional discrete fracture model is used to simulate infiltration into a variably saturated porous block containing a single vertical rough-walled fracture. The results show that flow system dynamics are considerably more sensitive to matrix properties, namely, hydraulic conductivity and antecedent moisture content, than fracture properties. A high degree of fracture-matrix interaction restricts preferential flow down the fracture and decreases the influence of fracture roughness. The study results suggest that aperture variability within individual fractures may be neglected when modeling water flow through unsaturated soils. Nevertheless, the fracture plays an important role in water movement and controls the vertical flux of a surface applied tracer.