ABSTRACT Microcystis aeruginosa is a toxic cyanobacteria species that is often abundant during cyanobacterial harmful algal blooms (cyanoHABs) in freshwaters. This study examined how growth on different nitrogen substrates influences the exometabolome of toxic and non‐toxic strains of M. aeruginosa . We used untargeted metabolomics, with liquid chromatography‐mass spectrometry of metabolites followed by feature‐based molecular networking and in silico metabolite annotation. Molecules released by M. aeruginosa varied based on the type of N substrate provided: the exometabolomes of cultures grown on ammonium and urea were more similar to each other and distinct from those grown on nitrate, suggesting that different assimilatory energetic requirements between reduced and oxidised N substrates are an important driver of exometabolome composition. Amino acids and peptides were the dominant compound class among metabolites that were significantly different between N treatments, but responses to N substrate were also reflected in altered extracellular concentrations of lipids, cyanotoxins, and photoprotectants. These differences in the molecular‐level response to the type of N substrate supplied support that environmental factors like changing N availability and oxidative stress may synergistically influence M. aeruginosa strain fitness and community succession, as well as interactions between M. aeruginosa strains and other bacteria or cyanobacteria in the bloom community.