||Bioenergy is necessary to meet future world-wide energy demands while helping to offset the global impacts of increased carbon dioxide from traditional fossil fuels. Options for producing bioenergy without adversely impacting food, water, and other environmental resources are currently being explored including using woody biomass as feedstock. Key issues among stakeholders include soil and water quality and loss of biodiversity as collecting small-diameter woody biomass may significantly alter post-timber harvesting landscapes. Linkages between land use changes and runoff, erosion, and sedimentation processes in river basins are known to exist but little is known about how land use changes impact the entire ecological function of the watershed. The objectives of this study were to explore using changes in microbial soil populations as a function of woody biomass removal treatment scenarios to determine potential changes in long-term water export and nutrient ecology, measuring changes in sediment erosion and collecting data to measure changes in infiltration/evaporation. This will help us understand the environmental impacts of biomass removal in the production of jet fuel and will be the start of holistic river basin management strategies focused on hydrologic implications of the entire food web. Microbial population data were collected from 28 one-acre plots subject to different land treatments and analyzed statistically to evaluate a null hypothesis that changes in biomass removal do not impact subsurface environment. Finger printing analysis and bio diversity index were calculated to understand the impact from a biological point of view. Sediment erosion was estimated using the WEPP model and then we tried to compare the model result with observed result. Results indicate that significant removal of biomass is possible without statistically altering the microbial food web, and the sites possessed such unique characteristics for which parameterization of the WEPP model for the whole Pacific Northwest is not possible using the data of these sites. Longer term analysis of soil infiltration and site runoff are needed to quantify the role of climate condition on these findings.