Vernal pools are small depressional wetlands found in seasonal climates throughout the world. In California, they are among the few ecosystems still dominated by native flora and are critical habitat for numerous endemic and rare species. In this study, we show that geology is a dominant control on the physical and chemical hydrology of contrasting vernal pools on clay-rich and hardpan soils, the two most common types of vernal pools in the Central Valley, California. The vernal pools on clay-rich soils formed on alluvium derived primarily from sedimentary and metasedimentary rocks of marine origin and deposited in relatively low-gradient environments. The clay-rich soils are fine grained and moderately to strongly saline and sodic. The vernal pools on clay-rich soils are perched surface-water systems in which surface waters are relatively saline, sodic, and turbid and in which primary productivity may be nitrogen and light limited. The vernal pools on hardpan soils formed on alluvium derived primarily from coarse-grained igneous rocks and deposited in relatively high-gradient environments. Surface soils are coarse grained and underlain by a clay-rich argillic horizon and a silica- and iron-cemented duripan. The vernal pools on hardpan soils are surface-water and perched ground-water systems in which surface waters are relatively fresh and non-turbid and in which primary productivity may be phosphorus limited. While surficially similar, these vernal pools differ in their physical and chemical hydrology, and therefore should be treated differently in resource conservation, restoration, and management efforts.