Various interactions between algae and bacteria significantly influence the primary productivity of aquatic ecosystems, algae community composition, dynamics of competition and succession among algal species, and development of algal blooms. Metabolic coupling facilitates the cycling of crucial biogenic elements, including carbon, nitrogen, phosphorus, and sulfur, throughout the water column. In freshwater ecosystems, cyanobacterial blooms remain a persistent and essential threat to the aquatic environment health, and a steady state of weekly cyanobacterial bloom occurrence has developed in many water bodies. Interactions and metabolic exchanges between cyanobacteria and associated bacteria are pivotal to carbon and nitrogen cycles in aquatic systems and are modulated by environmental factors. This review examined the implications of cyanobacteria-bacteria interactions on cyanobacterial growth, toxicity, colony persistence, and diversity and the factors influencing cyanobacteria-bacteria interactions. The influences of carbon- and nitrogen-related functional microbial communities on the cycling processes within the phycosphere and the broader aquatic ecosystem were assessed. Moreover, the effects of cyanobacterial community particles, attachment and environmental factors such as temperature, nutrient levels, pollutants, and iron, sulphur and phosphorus, on the metabolic linkage and transfer of carbon and nitrogen between cyanobacteria and bacteria were summarized, and the feedback mechanisms of these interactions were discussed. Additionally, principal research methodologies for studying algae-bacteria interactions and carbon and nitrogen transformation processes and fluxes between algae and bacteria were explored. Advances in these studies may provide insights into the mechanisms of algae-bacteria interactions mediated by cyanobacterial blooms and the microbiological processes underlying the cycling and fluxes of biogenic elements in water bodies.