This research uses a series of physiological models, empirical measurements, and archived data to evaluate biogeochemical controls over coupled carbon-water cycles across California's managed and natural systems. By making measurements from the individual plant to the ecosystem scale, this work seeks to expand our understanding of the variable drivers of productivity-efficiency tradeoffs at these different scales. First, we use a series of latitudinal and altitudinal transects established across the California Sierra Nevada to study the effects of climatic and edaphic gradients on intrinsic water use efficiency of 9 dominant tree species. Changes in plant-soil-atmosphere relations are related through measures of productivity, nutrient cycling, and soil physical properties to elucidate the interacting roles of species traits and stand scale properties in determining tree level efficiency. This first chapter establishes the role of geologic controls over efficiency while quantifying species specific ranges to help define the limits of their plasticity. Following this evaluation of forest carbon-water relations, we investigate how soil, climate, and management properties impact those cycles in an agricultural system. Using a dataset describing wheat production in California from 1981 to present, the competing roles of environmental stress and management are evaluated to determine the influence of shifts in climate variability on yield, agronomic water use efficiency, and nitrogen use efficiency. This is especially important because in recent decades there has been a stagnation in productivity of a number of important California crops, including wheat, despite continued advances in genetic variety, irrigation management, and fertilizer technology. We control for these factors, and show that despite intensive management to minimize stress, that climate and atmospheric CO2 exert a significant control over wheat productivity and efficiency across California. Further, we find that over time there has been a shift in yield response curves, indicating that over time more water and nitrogen have become necessary to maximize production. Last, in recognition that the intricacies of carbon-water relations are difficult to measure, a new method for measuring plant water relations is developed and evaluated. There is a litany of research regarding the use of stable isotope proxies for plant-water relations, but most of the work addresses only plant scale shifts in physiology. Recent work has shown the power of lipid biomarkers for deducing ecosystem to continental scale shifts in hydrology throughout recent millennia, but has only focused on carbon and hydrogen isotope ratios. Combined analysis of hydrogen and oxygen isotope ratios of plant water yields deuterium excess, a variable that helps understand the balance of evaporation and transpiration in a system. Through an incubation of lipid compounds in isotopically enriched water, we show that oxygen isotopes of organic matter are stable to exchange, which suggests that soil and sedimentary organic material has a non-exchangeable pool of compounds which is related to plant water status and thus can be used to study integrated ecosystem scale plant water relations over time.