Major and trace element geochemistry of sediment cores of “legacy” deposits (i.e., sediments eroded from upland areas starting in Colonial times, reflecting intensive land use, that have altered pre-Colonial environments and are impairing modern environments) from behind former mill dams in different land-use sub-watersheds of the Yellow Breeches Creek (Cumberland County, Pennsylvania, USA) provide insight into the origins of elements with multiple natural and anthropogenic sources. In comparing a forested land-use watershed with an agriculturally affected one, we find similar elemental ratios with Al for pre-settlement and early legacy sediments, but increasing trends of nutrient elements and select trace metals through time in the agriculturally affected legacy deposit. Likely sources of excess P, Cu, and Pb over background are fertilizer, pesticides, and other soil amendments. Pb trends show smaller increases over time in the forested land-use subwatershed, mostly due to the input of leaded gasoline emissions to the atmosphere and ubiquitous fallout to all watersheds. The agriculturally affected subwatershed cores show significantly more Pb, suggesting multiple sources. The continued remobilization of legacy sediments from thousands of mill ponds in the eastern United States suggests that this source of nutrients and trace elements may add significantly to the degradation of downstream ecosystems such as the Chesapeake Bay.