Soil and water pollution is a major problem that has a negative impact on ecosystems and human health in particular. In the bioremediation processes, the application of photosynthetic microorganisms, including cyanobacteria, is a direction of action addressed with increasing frequency in the context of further development and improvement of environmentally friendly techniques needed for detoxification of soils and waters polluted with low concentrations of toxic elements, since they pose a challenge for traditional treatment methods. In the present study, the removal of copper and other metal ions from multielement systems by three generations of Nostoc linckia is discussed. Changes in the biochemical composition of the nostoc biomass, which accumulates metal ions, were monitored. Neutron activation analysis was applied to assess Cu, Fe, Ni, and Zn accumulation by biomass, as well as to determine the biochemical composition of biomass after specific biochemical methods were used. The capacity of the accumulation of copper and other metal ions from multi-elemental systems by cyanobacteria Nostoc linckia was high and increased over two cycles of biomass growth in the systems Cu-Fe-Ni and Cu-Fe-Zn and over three cycles in Cu-Fe and Cu-Fe-Ni-Zn systems. It constituted 1720–10,600 µg metal/g depending on the system and cycle of cultivation. The accumulation of Fe, Ni, and Zn also increased over the generations of nostoc. The process of metal accumulation was demonstrated by a significant change in the biomass biochemical composition. Cyanobacteria Nostoc linckia possess a pronounced capacity of copper and other metal ion accumulation from multimetal systems and showed an increased resistance in environments polluted with heavy metals.