A study was initiated to investigate the sustainability effects of intercropping switchgrass ( L.) in a loblolly pine ( L.) plantation. This forest-based biofuel system could possibly provide biomass from the perennial energy grass while maintaining the economics and environmental benefits of a forest managed for sawtimber. Operations necessary for successful switchgrass establishment and growth, such as site preparation, planting, fertilizing, mowing and baling, may affect hydrology and nutrient runoff. The objectives of this study were (i) to characterize the temporal effects of management on nutrient concentrations and loadings and (ii) to use pretreatment data to predict those treatment effects. The study watersheds (∼25 ha each) in the North Carolina Atlantic Coastal Plain were a pine/switchgrass intercropped site (D1), a midrotation thinned pine site with natural understory (D2), and a switchgrass-only site (D3). Rainfall, drainage, water table elevation, nitrogen (total Kjedahl N, NH-N, and NO-N), and phosphate were monitored for the 2007-2008 pretreatment and the 2009-2012 treatment periods. From 2010 to 2011 in site D1, the average NO-N concentration effects decreased from 0.18 to -0.09 mg L, and loads effects decreased from 0.86 to 0.49 kg ha. During the same period in site D3, the average NO-N concentration effects increased from 0.03 to 0.09 mg L, and loads effects increased from -0.26 to 1.24 kg ha. This study shows the importance of considering water quality effects associated with intensive management operations required for switchgrass establishment or other novel forest-based biofuel systems.