Cyanobacteria are photoautotrophic prokaryotes that perform oxygenic photosynthesis; their morphology includes unicellular, colonial, and multicellular filamentous forms. Because of their wide metabolic diversity, these microorganisms inhabit many ecosystems, including extreme environments, producing various metabolites of economic importance. Cyanobacteria are major components of soil microbiota and have many applications in agriculture, including their use as biofertilizers, biopolymers, biocontrol agents, protein sources, and food supplements. Diazotrophic cyanobacteria have the potential to fix atmospheric nitrogen, making it accessible for plant uptake, thus emerging as potential biofertilizers for sustainable agriculture development. Extracellular polysaccharides and plant growth-promoting substances produced by cyanobacteria enrich soil organic carbon, enhance microbial aggregation, improve soil stability, and promote seed germination. Biofertilization is a promising, environmentally friendly strategy to mitigate the spread of desertification and restore salt-affected arid or semi-arid soils. Cyanobacteria are also promising candidates for the bioremediation of contaminated soils and aquatic systems. Organic phosphate and nitrate accumulation in water bodies, resulting from agricultural practices and industrial activities, can lead to eutrophication and oxygen depletion, harming aquatic organisms. Certain cyanobacterial strains can help mitigate these impacts by reducing excess phosphate, nitrate, heavy metals, and oxidizing complex organic pollutants, such as pesticides. Nevertheless, challenges remain in improving productivity and reducing costs in bioremediation applications. Therefore, selecting and appropriately optimizing cyanobacterial strains or consortia are crucial to enhance large-scale production to support soil and water restoration in sustainable agricultural systems.