The effects of the structural features of the thallus and the lichen–substratum interface on soil water infiltration were investigated using low temperature scanning electron microscopy and scanning electron microscopy with backscattered electron imaging. Two morphologically different lichen species were examined, the crustose Diploschistes diacapsis and the squamulose Squamarina lentigera. Water distribution within lichen-forming soil crusts explains the results of earlier infiltration studies. Several anatomical features of the upper cortex gave rise to similar impervious characteristics of the thallus. The fungal material comprising the lichen thallus showed significant hydrophobic features and only when in contact with calcium oxalate crystals or minerals in the soil was this material able to retain water. The lichen–substratum interface appears to play an important role in the hydric strategy of these lichens which in turn affects the penetration of water into the soil.