Surplus nitrogen (N) estimates, principal component analysis (PCA), and end-member mixing analysis (EMMA) were used in a multisite comparison contrasting the fate of N in diverse agricultural watersheds. We applied PCA-EMMA in 10 watersheds located in Indiana, Iowa, Maryland, Nebraska, Mississippi, and Washington ranging in size from 5 to 1254 km² with four nested watersheds. Watershed Surplus N was determined by subtracting estimates of crop uptake and volatilization from estimates of N input from atmospheric deposition, plant fixation, fertilizer, and manure for the period from 1987 to 2004. Watershed average Surplus N ranged from 11 to 52 kg N ha⁻¹ and from 9 to 32% of N input. Solute concentrations in streams, overland runoff, tile drainage, groundwater (GW), streambeds, and the unsaturated zone were used in the PCA-EMMA procedure to identify independent components contributing to observed stream concentration variability and the end-members contributing to streamflow and NO₃ load. End-members included dilute runoff, agricultural runoff, benthic-processing, tile drainage, and oxic and anoxic GW. Surplus N was larger in watersheds with more permeable soils (Washington, Nebraska, and Maryland) that allowed greater infiltration, and oxic GW was the primary source of NO₃ load. Subsurface transport of NO₃ in these watersheds resulted in some removal of Surplus N by denitrification. In less permeable watersheds (Iowa, Indiana, and Mississippi), NO₃ was rapidly transported to the stream by tile drainage and runoff with little removal. Evidence of streambed removal of NO₃ by benthic diatoms was observed in the larger watersheds.