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Determining the interaction between surface runoff and subsurface hydrology has been hindered by our inability to characterize the subsurface stratigraphy on a watershed scale. Over 40 km of ground-penetrating radar (GPR) data were collected and evaluated in determining subsurface stratigraphy and flow patterns on a 20 ha research site in Beltsville, Maryland. The research site has four watersheds with a confining clay lens that varies in depth between 0.9 m and 3.5 m from the soil surface. The watersheds have similar textures, organic matter content, as determined with over 1,700 soil cores. Yield distributions were also similar. Although the surface slope was greater on one of the watersheds, slope alone could not explain why it also had a nitrate runoff flux that was 18 times greater than the other watersheds. GPR data revealed that this watershed had subsurface flow patterns that allowed seepage zones to exist. This study demonstrates the impact subsurface stratigraphy can have on surface chemical runoff fluxes.