The estimate of soil fertility, namely, water and nutrient availability, and biological activity, is usually made considering soil as being uniform in the reference layers and its characteristics varying in space according to gradients. The potential fertility is thus estimated for homogeneous soil volumes. However, soil layers and horizons are mainly not homogeneous and discontinuous. The soil rooting capacity, in particular, can be limited by the presence of obstacles, such as bedrock, cemented layers and stones, but also by soil masses which are so dense that cannot be penetrated by roots. These compact masses are almost always overlooked and not considered in the estimation of soil fertility. In this work, an innovative method, which considers the presence of clods in the soil volume, is proposed for estimating the potential soil rooting capacity. Clods are the soil masses or aggregates which are too compact to be explored by roots. Correcting the values of available nutrients and water holding capacity according to the potential soil rooting capacity increases its correlation with plant phenology and the agronomic result. The method could be particularly useful when planning the operations to be carried out before the planting of specialized tree crops.