The structural soil heterogeneity caused by agro-technical measures can have a large impact on water flow and sediment transfer. The main objective of the paper was to evaluate how the presence of different structural zones in the soil’s arable layer affects the initiation of preferential water flows in the soil and to assess the impact of the herbicide isoproturon degradation rate on the dynamics of its transport. Long-period data from the Polish trial (QualiAgro, 2004 - 2010) which applies compost obtained through urban biological waste recycling were used for the calibration and verfication of the numerical model HYDRUS-2D. Water flow and isoproturon dynamics were successfully simulated after the calibration of hydraulic parameters and temporal optimization of the isoproturon degradation rate. Preferential flows occured in interfurrows due to a high compost porosity resulting from the flow’s direction around the soil’s compacted zones. On the other hand, the addition of compost obtained through recycling of sewage sludge and green biological waste increased isoproturon degradation and sorption in areas containing the highest compost amounts, thus reducing its transport.