Land quality and land use are inextricably linked with water and energy. The extent to which this linkage flourishes depends on the ‘where’ (land marginality), ‘how’ (management) and ‘what’ (feedstock) we choose for producing biofuels.  To understand the effect of soil and land quality on yield, and water and energy footprints, we studied these relationships on seven large scale sites (9-20 ha) converted from either conservation reserve program (CRP) or conventional agricultural land use to soybean production for biofuel. Unmanaged CRP grassland at the same geographical location was used as the reference. We categorized the sites into different marginality rating by proposing a land marginality index (LMI) which was based on land capability classification, land slope, and soil erosion and tolerance factors (extracted from geographic soil survey, SSURGO, database), and a principle components based soil quality index (SQI). We studied the consumptive water use and net ecosystem productivity (NEP) using eddy-covariance flux monitoring towers on each site. The water and energy footprints of the sites were well related to the indices developed.  Aboveground net primary productivity was inversely related to LMI and positively related to SQI. Water and energy footprints increased with LMI and decreased with SQI. The water footprints for grain, biomass and energy production were higher on lands converted from agricultural land use compared with those converted from the CRP land. The sites which were previously in the CRP had higher SQI than those under agricultural land use, showing that land management affects water footprints through soil quality effects. The analysis of biophysical characteristics of the sites in relation to water and energy use suggests that crops and management systems similar to CRP grasslands may provide a potential strategy to grow biofuels that would minimize environmental degradation while improving the productivity of marginal lands.