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The over‐enrichment of nitrogen (N) in the environment has contributed to severe and recurring harmful cyanobacterial blooms, especially by the non‐N₂‐fixingMicrocystisspp. N chemical speciation influences cyanobacterial growth, persistence and the production of the hepatotoxin microcystin, but the physiological mechanisms to explain these observations remain unresolved. Stable‐labelled isotopes and metabolomics were employed to address the influence of nitrate, ammonium, and urea on cellular physiology and production of microcystins inMicrocystis aeruginosaNIES‐843. Global metabolic changes were driven by both N speciation and diel cycling. Tracing¹⁵N‐labelled nitrate, ammonium, and urea through the metabolome revealed N uptake, regardless of species, was linked to C assimilation. The production of amino acids, like arginine, and other N‐rich compounds corresponded with greater turnover of microcystins in cells grown on urea compared to nitrate and ammonium. However,¹⁵N was incorporated into microcystins from all N sources. The differences in N flux were attributed to the energetic efficiency of growth on each N source. While N in general plays an important role in sustaining biomass, these data show that N‐speciation induces physiological changes that culminate in differences in global metabolism, cellular microcystin quotas and congener composition.