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Humans have altered Earth’s nitrogen cycle so dramatically that reactive nitrogen (Nr) has doubled. This has increased Nr in aquatic ecosystems, which can lead to reduced water quality and ecosystem health. Apportioning sources of Nr to specific ecosystems, however, continues to be challenging, despite this knowledge being critical for mitigation and protection of water resources. Moreover, agricultural activities, specifically nitrate- and ammonium-based fertilizer use, are contributing most (B60%) Nr, and data from other North American alpine lakes suggest this is a widespread phenomenon. Our findings offer a pathway towards more effective mitigation, but point to challenges in balancing food production with protection of important water resources.