Water flow in structured clay soils is strongly influenced by the presence and geometry of macropores. This study was conducted to develop a method that could measure bypass flow, provide a morphological analysis of the water-conducting macropore system, and combine physical and morphological data in a simulation model for prediction purposes. The effects of different physical boundary conditions on bypass flow, such as rain intensity, the conductivity of the soil, soil microrelief and initial pressure head in the soil, were tested with a computer-controlled measuring device. Measurements were carried out on large undisturbed soil cylinders in the laboratory. Macropore geometry was subsequently characterized by using fractal dimensions of staining patterns on horizontal cross-sections and was a very important parameter to explain the measured outflow. A pedotransfer function, based on this geometry, was used to calculate the time of initial breakthrough at the bottom of the soil cylinders. This pedotransfer function was then used in a computer model which simulated bypass flow successfully in 15 large soil columns. The total amount of outflow was not directly influenced by rain intensity but more by the amount of rain applied.