The water storage capacity of the root zone determines whether plants survive dry periods and controls the partitioning of precipitation into streamflow and evapotranspiration. It is currently thought that top-down, climatic factors are the primary control on this capacity via their interaction with plant rooting adaptations. However, it remains unclear to what extent bottom-up, geologic factors can provide an additional constraint on storage capacity. Here we use a machine learning approach to identify regions with lower than climatically expected apparent storage capacity. We find that in seasonally dry California these regions overlap with particular geologic substrates. We hypothesize that these patterns reflect diverse mechanisms by which substrate can limit storage capacity, and highlight case studies consistent with limited weathered bedrock extent (melange in the Northern Coast Range), toxicity (ultramafic substrates in the Klamath-Siskiyou region), nutrient limitation (phosphorus-poor plutons in the southern Sierra Nevada), and low porosity capable of retaining water (volcanic formations in the southern Cascades). The observation that at regional scales climate alone does not ‘size’ the root zone has implications for the parameterization of storage capacity in models of plant dynamics (and the interrelated carbon and water cycles), and also underscores the importance of geology in considerations of climate-change induced biome migration and habitat suitability.