The Critical Zone (CZ) is the surficial layer of the planet that sustains life on Earth and extends from the base of the weathered bedrock to the top of the vegetation canopy. Its structure influences water fluxes, biogeochemistry and vegetation. In this dissertation, I explore the relationships between climate, water fluxes, vegetation dynamics, biogeochemistry, and effective energy and mass transfer fluxes (EEMT) in a semi-arid critical zone. This research was carried out in the upper Jemez River Basin in northern New Mexico across gradients of climate and elevation. The main research objectives were to (i) quantify relations among inputs of mass and energy (EEMT), hydrological and biogeochemical processes within the CZ, (ii) determine water fluxes and vegetation dynamics in high elevation mountain catchments with different terrain aspect and solar radiation, and (iii) study temporal variability of climate and its influence on the CZ water availability, forest productivity and energy and mass fluxes. The key findings of this study include (i) significant correlations between EEMT, water transit times (WTT) and mineral weathering products around Redondo Peak. Significant correlations were observed between dissolved weathering products (Na⁺ and DIC) and maximum EEMT. Similarly, ³H concentrations measured at the springs were significantly correlated with maximum EEMT; (ii) terrain aspect strongly controls energy, water distribution, and vegetation productivity in high elevation ecosystems in catchments draining different aspects of Redondo Peak. The predominantly north facing catchment, when compared to the other two eastern catchments, receives less solar radiation, exhibits less forest cover and smaller biomass, has more surface runoff and smaller vegetation water consumption. Furthermore, the north facing catchment showed smaller NDVI values and shorter growing season length as a consequence of energy limitation, and (iii) from 1984 to 2012 a decreasing trend in water availability, increased vegetation water use, a reduction in both forest productivity and EEMT was observed at the upper Jemez River Basin. These changes point towards a hotter, drier and less productive ecosystem which may alter critical zone processes in high elevation semi-arid systems.