Bloom-forming cyanobacteria play a pivotal role in aquatic nitrogen cycling due to their ability to fix atmospheric nitrogen and assimilate various combined nitrogen sources. This chapter explores the molecular, biochemical, and ecological dimensions of nitrogen fixation and assimilation in these organisms. We examine the structure and regulation of the nitrogenase enzyme complex, the genetic control of heterocyst differentiation, and adaptive strategies to overcome oxygen sensitivity. Additionally, the chapter discusses major nitrogen assimilation pathways, including nitrate/nitrite reduction, ammonium transport, and the GS-GOGAT cycle, alongside their regulation through signal transduction networks such as NtcA and PII proteins. Emphasis is placed on physiological and molecular adaptations during bloom conditions, including nutrient sensing, diurnal metabolic coordination, nitrogen storage, and interactions with carbon and phosphorus metabolism. Understanding these integrated pathways is critical to predicting bloom dynamics and managing eutrophication in aquatic ecosystems.