The impact of varying soil micromorphology on soil hydraulic properties and, consequently, on water flow and herbicide transport observed in the field is demonstrated on three soil types. The micromorphological image of a humic horizon of Haplic Luvisol showed higher-order aggregates. The majority of detectable pores corresponding to the pressure head interval between −2 and −70 cm were highly connected, separating higher-order peds with small intrapores that possibly formed zones with immobile water. Herbicide was regularly distributed in this soil. The majority of detectable large capillary pores in a humic horizon of Greyic Phaeozem were separated and affected by clay coatings and fillings. The herbicide transport in this soil was highly affected by preferential flow. Macropores corresponding to pressure heads higher than −2 cm were detected in a humic horizon of Haplic Cambisol. However, preferential flow only slightly influenced the herbicide transport in this soil. Single-porosity and either dual-porosity or dual-permeability flow and transport models in HYDRUS-1D were used to estimate the soil hydraulic parameters from laboratory multistep outflow and ponded infiltration experiments via numerical inversion and to simulate the herbicide transport experimentally studied in the field. Appropriate models were selected on the basis of the soil micromorphological study.