This paper presents initial investigations of a new approach to monitor ecosystem processes in complex terrain on large scales. Metabolic processes in mountainous ecosystems are poorly represented in current ecosystem monitoring campaigns because the methods used for monitoring metabolism at the ecosystem scale (e.g., eddy covariance) require flat study sites. Our goal was to investigate the potential for using nocturnal down-valley winds (cold air drainage) for monitoring ecosystem processes in mountainous terrain from two perspectives: measurements of the isotopic composition of ecosystem-respired CO2 (delta13C(ER)) and estimates of fluxes of CO2 transported in the drainage flow. To test if this approach is plausible, we monitored the wind patterns, CO2 concentrations, and the carbon isotopic composition of the air as it exited the base of a young (approximately 40 yr-old) and an old (>450 yr-old) steeply sided Douglas-fir watershed. Nocturnal cold air drainage within these watersheds was strong, deep, and occurred on more than 80% of summer nights. The depth of cold air drainage rapidly increased to tower height or greater when the net radiation at the top of the tower approached zero. The carbon isotope composition of CO2 in the drainage system holds promise as an indicator of variation in basin-scale physiological processes. Although there was little vertical variation in CO2 concentration at any point in time, we found that the range of CO2 concentration over a single evening was sufficient to estimate delta 13C(ER) from Keeling plot analyses. The seasonal variation in delta 13C(ER) followed expected trends: during the summer dry season delta 13C(ER) became less negative (more enriched in 13C), but once rain returned in the fall, delta 13C(ER) decreased. However, we found no correlation between recent weather (e.g., vapor pressure deficit) and delta 13C(ER) either concurrently or with up to a one-week lag. Preliminary estimates suggest that the nocturnal CO2 flux advecting past the 28-m tower is a rather small fraction (<20%) of the watershed-scale respiration. This study demonstrates that monitoring the isotopic composition and CO2 concentration of cold air drainage at the base of a watershed provides a new tool for quantifying ecosystem metabolism in mountainous ecosystems on the basin scale.