The Earth system is undergoing extensive change, with important implications for human health, resource management, ecosystem services and the environment. The ability to predict these changes and their impacts on time scales of months to a decade is becoming increasingly important. Key to improving the predictability of Earth system behavior over these time scales is an improved understanding of the coupling between water, energy and biogeochemical cycles in a multi-scale modeling framework. Robust predictions at these time scales require coordinated modeling, observations and process studies that explicitly address the coupled water, energy and biogeochemical cycles at multiple temporal and spatial scales. The BEACHON (Biosphere-atmosphere-hydrosphere-interactions of Energy, Aerosols, Carbon, Organics, and Nitrogen) project initiated two complementary field studies in a ponderosa pine woodland to enhance understanding of the roles of biogenic volatile organic compounds (BVOC), aerosols, nitrogen trace gases and oxidants in linking and regulating the carbon and water cycles. The BEACHON-ROCS (Rocky mountain Organic Carbon Study) was conducted in summer 2010 and was focused on understanding BVOC oxidation and the impact on atmospheric oxidants. The BEACHON-RoMBAS (Rocky Mountain Biogenic Aerosol Study) will be conducted in summer 2011 and will be focused on understanding the formation, growth and properties of biogenic organic aerosol. This special issue will highlight field and modeling investigations associated with the BEACHON ROCS and ROMBAS studies.