Soil microbial activity is responsible for most of the decomposition and nutrient cycling that occurs in any terrestrial ecosystem. Although microbial activity is tightly controlled by water availability in arid ecosystem, microbial dynamics are nonetheless crucial for ecosystem processes when soil moisture is available during "windows of opportunity" in arid ecosystems. The Pine Canyon Watershed Program was established at Big Bend National Park in 1995, as part of a network of watershed sites in National Parks, to determine seasonal and spatial patterns of microbial activity, nutrient dynamics, hydrology, and impacts of climate change and anthropogenic inputs at the watershed level. The Pine Canyon Watershed extends over 19 kilometers and encompasses five major vegetation zones that are common in the Chihuahuan Desert: Lowland Scrub (793 m); Creosotebush-Bajada (1010 m); Sotol-Grassland (1526 m); Closed Canopy Oak-Forest (1824 m), and high elevation Oak-Pine Forest (2098 m). Two 100 X 30 m belt transects have been established in each vegetation zone and 10 soil samples are taken from each transect in January and August to capture periods of maximum soil moisture and temperature variation. Data on soil microbial dynamics and associated nutrient and soil edaphic characteristics have been collected since 1996. Two aspects of microbial activity are measured from each soil sample, microbial biomass, and bacterial functional diversity. These parameters provide insights into the impacts of climate and anthropogenic inputs on the status of the soil microbiota across the watershed. Microbial biomass and functional diversity are highest in the Oak Forest, followed by the high elevation Oak-Pine Forest. The Lowland Scrub and Creosotebush-Bajada sites have the lowest microbial biomass and functional diversity with the Sotol-Grassland sites intermediate between the forest and shrub dominated sites. The Sotol-Grassland site is very sensitive to atmospheric inputs of nitrogen, while the low elevational sites have been impacted by drought stress for the last four years. Continued drought and inputs of nitrogen will lead to a continued decline in microbial activities in the low elevation sites, and the potential for eventual shift in plant species along this part of the watershed as microbial dynamics continue to change.