Landscapes composed of wetlands and uplands contain a variety of production environments.  Bioenergy crop species may be uniquely suited for different field and landscape positions based on existing soil properties.  This study is designed to observe soil quality patterns within uplands and wetlands in agricultural fields in transition to bioenergy production and compared with a nearby remnant prairie. Agricultural lands have substantially changed properties from their prairie origins. Virgin prairie soil undergoes many physical and chemical changes after cultivation and these effects are intensified over long periods. We examined soil organic carbon in relationship to dynamic soil properties including POM (Particulate Organic Matter), WAS (wet aggregate stability), and microbial activity between a remnant prairie and former cropland undergoing transition to perennial bioenergy feedstock production. Both sites represent a heterogeneous landscape including wetlands intermingled with uplands.  The agricultural landscape includes eroded soils and previously drained wetlands. The uplands were examined at four landscape positions including the summit, upper shoulder, backslope, and foot slope. In addition to the uplands, two wetland classes were compared between the remnant prairie and the formerly cultivated site at three positions based on elevation: high point, mid point, and low point. Higher soil organic carbon, aggregate stability, and microbial activity were observed in the remnant prairie due to the loss of labile carbon associated with tillage. Wetlands present within the remnant prairie contained greater organic carbon pools than those wetlands with a long history of cropping due to oxidation from cultivation after drainage. Management of land in transition from cropland to grassland can also influence carbon dynamics.  In a second study carbon dynamics of previously cropped lands planted to grass differed depending on whether the grass was burned, mowed, or harvested over a nine year period.