The cyanobacterium Nostoc linckia was used to study the biotechnology of selenium nanoparticles synthesis for the first time. The experimental conditions of the nanoparticle production by the studied cyanobacteria in aqueous cobalt selenite solutions were examined. Neutron activation analysis allowed characterization of the dynamics of accumulation of the total selenium quantity by Nostoc linckia. Scanning Electron Microscope images demonstrated extracellular formation of amorphous nanoparticles. Released selenium nanoparticles ranged in size from 10 to 80 nm. The changes of essential parameters of biomass (proteins, lipids, carbohydrates, and phycobilin) content during the nanoparticle formation were assessed. During the first 24 h of nanoparticle synthesis, a slight decline of proteins, lipids and carbohydrates content in the biomass was observed. The most extensive was the process of phycobilin degradation. Furthermore, all biochemical component content as well as an antioxidant activity of the biomass extracts significantly decreased. The obtained substance of Nostoc biomass with selenium nanoparticles may be used for medical, pharmaceutical and technological purposes.