Nitrogen cycling has been evaluated across a depth transect in the late Paleoproterozoic Animikie Basin (North America), spanning the end of Earth’s final period of global iron precipitation, and a major transition to euxinic conditions in areas of high productivity. Sediments from near shore, where productivity was highest, have δ15N compositions up to ∼3‰ higher than at more distal sites. This suggests that as NH4+ mixed vertically upward into the oxic photic zone from the anoxic ocean interior, it was either assimilated by organisms or oxidized. Subsequent enhanced production of N2 by denitrification or anammox (anaerobic ammonium oxidation) led to the observed increase in δ15N close to shore. Any deficit in biologically available N was overcome by N2-fixing organisms, but the input of N with low δ15N from this process did not overwhelm the increase in δ15N from denitrification. Because there is no evidence for conditions of severe N stress arising from trace metal limitation (particularly Mo) of N fixation during the transition to euxinic conditions, losses of N were either very small (potentially because low O2 levels limited NH4+ oxidation), or alternative pathways that retained N were important. The fact that Mo appears to have remained bioavailable for N fixation, either suggests that the extent or severity of sulfidic water column conditions was not sufficient to quantitatively sequester Mo on a global scale, or that rivers directly delivered Mo to surface waters on the inner shelf. The effects of N2 fixation on δ15N increased to more distal parts of the shelf, consistent with models invoked for modern upwelling zones over broad continental margins.