Nitrogen (N) limits primary production in many terrestrial and aquatic systems, a paradox in a world with 78% N
2
in the atmosphere. Nitrogen has nine valence states ranging from reduced (−3, NH
3
, amino groups) to oxidized (+5, NO
3
−
), creating opportunities for energy‐yielding microbial transformations of N along redox gradients. Anthropogenic N additions increase plant production and food supplies on land, but simultaneously result in contaminated drinking water, algal blooms, and hypoxia in adjacent waters. Management of these problems is often informed by N flux measurements and budgets. However, in watershed N budgets, measured N inputs typically exceed measured stream output, leading to the conundrum of “missing N.” The missing N is either stored internally within watersheds or lost to the atmosphere as N gases (NH
3
, N
2
, N
2
O, NO). Measurements of both N storage and N gas fluxes have accounted for the missing N in a few cases, but there are few examples of complete N budgets because measurements of the spatially/temporally heterogeneous N pools and N gas fluxes are difficult at the watershed scale. Therefore, investigating watershed N budgets remains a fruitful area for future research to control the deleterious effects of anthropogenic N in aquatic systems.