Interrelationships between the pathways of inorganic nitrogen assimilation in the cyanobacterium Gloeothece can be described using a mechanistic mathematical model.

•  A mathematical model is described that simulates the major features of the interactions between different nitrogen (N)-sources in the nonheterocystous diazotrophic cyanobacterium Gloeothece. •  The interaction between ammonium and nitrate is related to the intracellular concentration of glutamine (GLN), which in turn is representative of cellular N-status. Development of nitrogenase activity is related to N-limitation but, once developed, continues for as long as there is sufficient glucan (carbon-reserve) in order to support N2 fixation and the assimilation of the resultant ammonium into amino acids. •  Nitrogenase activity decreases in response to elevated N-status and also to increased net oxygen evolution, in keeping with biochemical reality. The model describes the diel cycle of C and N2 fixation as seen under alternating 12 h light and 12 h darkness, and also the N2 fixation cycle of about 40 h duration seen in cells cultured in continuous illumination. •  This model has the potential to be adapted to describe N2 fixation in heterocystous cyanobacterium and in Trichodesmium.