Microalgae based processes have been actively studied in the last decades with perspective for food, feed, and source of chemicals such as biofuels. Most of the developments focused on monospecific culture of microalgae, with dedicated practices to avoid any contaminations. However, interactions between microalgae and bacteria are likely to enhance microalgae growth, provide more resilience to external changes and eventually limit external contaminations. But interactions within these natural ecosystems are still poorly understood and are affected by the environment. A photosynthetic marine ecosystem composed of the microalgae Dunaliella salina and the nitrogen fixing cyanobacteria Crocosphaera watsonii was therefore studied. A model was designed to represent the competition for light and the interactions with nitrogen between these two microorganisms. An allelopathic effect was noticed and a toxin production by C. watsonii was assumed and included in the model. Calibration was carried out with experimental data where cell densities and nitrate concentrations were measured. The predictions of the mathematical model accurately represented the experimental data. The model therefore highlighted the interactions within this artificial ecosystem. The model confirms that D. salina growth was limited by nitrate concentration and did not consume dissolved organic nitrogen produced by C. watsonii from its diazotrophic activity. D. salina and C. watsonii were competing for light, which favored D. salina and limited C. watsonii when grown in cocultures. The model supports the hypothesis that C. watsonii produced toxins enhancing D. salina mortality in the cocultures.