Recent studies have indicated that under certain conditions, most soils are water repellent to some degree, which impacts agricultural fields, pastures, forests, grasslands, and turf areas. Soil water repellency originates from amphiphilic molecules that reorient during contact with water. However, models to describe the flow in soils affected by time-dependent contact angle (CA(t)) are still lacking. The current study aims to close this gap. The measured CA(t) for an oleic acid-coated glass surface and a uniform capillary tube indicated that the initial CA was substantially higher for the latter. However, the rate of CA decrease was similar for both cases in spite of the fact that the contact area between the water and the tube wall continuously increases by the capillary rise. This indicates that the amphiphilic molecules reorientation at the vicinity of the contact line rather than at the wetted tube area controls the CA dynamics. A mathematical model for flow in a uniform and sinusoidal capillary tube with CA(t) < 90°that includes model for the reorientation of the amphiphilic molecules was introduced. The model for uniform case was successfully verified by comparison with measured capillary rise in a coated uniform tube. The simulations indicated that nonuniform pore geometry amplifies the effect of CA(t) on the capillary rise dynamics. The stepwise meniscus propagation in the sinusoidal capillary tubes is driven by the time for the meniscus to reach the converging section of the tube. The retardation in capillary rise increases with tube waviness.