The soil system stores more carbon than the atmosphere and biosphere combined. However, until recently, most studies on soil organic matter dynamics had focused on near surface soil organic carbon (C) dynamics with relatively little attention devoted to determining how much C and nitrogen (N) is stored in deep soil layers, and how climate influences deep soil organic C and N dynamics. Hence, our understanding of how climate influences the mechanisms that regulate the magnitude and direction of changes in deep soil organic matter remain incomplete. In my dissertation research, I studied soils that developed under four different climatic regimes along an elevation gradient on the western slopes of the Sierra Nevada in California (site of the Southern Sierra Critical Zone Observatory). Using soil samples that were collected from the surface down to bedrock contact (that extended to more than 10 m below the surface), I determined how climate regulates deep soil organic carbon and nitrogen stocks, chemical composition of organic matter, mean residence times of soil carbon and nitrogen at depth; and conducted statistical analyses to determine how variability of climate along the SSCZO bio-climosequence is related to a range of climatic variables. In the first chapter, I found that up to 78% of soil C is stored below a 0.3-m depth, with up to 29% of total C stored in saprock below 1.5 m. A conservative global scaling of these results illustrates that deep regolith stores over 200 Pg of organic carbon quantifying a previously unrealized organic carbon pool in the Earth system. In the second chapter, I dug deeper into C stabilization mechanisms and how climate impacts distribution of C in free and mineral protected pools of soil C. I discovered that the radiocarbon concentration of C in the topsoil and subsoil free particulate and subsoil mineral associated fractions had a statistically significant relationship with climate. However, the aggregate protected pool of C was not influenced by climate, suggesting that the free particulate and subsoil mineral associated fractions of subsoil C are vulnerable to changes in climate. The third chapter focused on dynamics of soil N in topsoil compared to subsoils and shows that climate imposes important controls on N in topsoil and subsoil free particulate and occluded fractions. The mineral associated N was not found to be sensitive to changes in climate. Overall, my dissertation research demonstrated both indirect and direct mechanisms through which climate can impact soil C and N dynamics from the topsoil to bedrock contact. I presented substantial evidence to refute the long-held assumption that subsoil organic matter does not respond to changes in atmospheric climate.