The goal of our research is to develop locally-acceptable, economically viable, watershed management systems that increase the sustainability of agriculture with respect to water quality, while improving the integrity of the aquatic and terrestrial ecosystems. We utilize observational and experimental approaches within managed and unmanaged ecosystems to assess the function of conservation buffers and improve their design and performance. Scales of study range from assessing microbial regulation of carbon and nitrogen cycling in stream and riparian systems to prioritizing the placement of conservation practices within a watershed.