Irrigation with treated waste water (TWW) is a common practice in agriculture, mainly in arid and semiarid areas as it provides a sustainable water resource available at all-season in general and at freshwater shortage in particular. However, TWW still contains abundant organic material which is known to decrease soil wettability, which in turn may promote flow instabilities that lead to the formation of preferential flow paths. We investigate the impact of long-term TWW irrigation on water wettability and infiltration into undisturbed soil cores from two commercially used orchards in Israel. Changes of water content during infiltration were quantitatively analysed by X-ray radiography. One orchard (sandy clay loam) had been irrigated with TWW for more than thirty years. In the other orchard (loamy sand) irrigation had been changed from freshwater to TWW in 2008 and switched back in some experimental plots to freshwater in 2012. Undisturbed soil cores were taken at the end of the dry and the rainy season to investigate the seasonal effect on water repellency and on infiltration dynamics in the laboratory. The irrigation experiments were done on field moist samples. A test series with different initial water contents was run to detect the influence on water movement at different wettabilities. In this study we show that the infiltration front stability is dependent on the history of waste water irrigation at the respective site and on the initial water content.