Trace metals, although found in small amounts in aquatic environments, significantly influence the physiology of cyanobacteria and are crucial to the health and functionality of aquatic ecosystems. This chapter delves into the complex interactions between trace metals such as iron, copper, and zinc and cyanobacteria, emphasizing both their necessary roles and potential toxic effects depending on concentration and bioavailability. After discussing the vital roles of trace metals in processes like photosynthesis, nitrogen fixation, and cellular respiration, this chapter moves on to examine the mechanisms that cyanobacteria use to manage these metals. This includes uptake regulation and the balancing act necessary to avoid the detrimental impacts of metal toxicity, such as oxidative stress and growth inhibition. The adaptability and resilience of cyanobacterial metal homeostasis systems are highlighted, showcasing their ability to thrive in varying environmental conditions. The chapter further analyzes how environmental factors, such as pH fluctuations, the presence of competing ions, and human activities, affect trace metal availability and cyanobacterial responses. The implications of these interactions are explored, particularly how they influence cyanobacterial bloom dynamics, species competition, and toxin production, all of which have significant consequences for water quality and public health. Concluding with a synthesis of recent research findings, the chapter presents a nuanced understanding of trace metal interactions in cyanobacterial ecology. It also outlines promising research directions and management practices aimed at mitigating harmful blooms while supporting robust and diverse microbial communities in aquatic systems.