Phosphorus plays a pivotal role in regulating the growth and composition of phytoplankton communities and is a primary driver of eutrophication and harmful algal blooms (HABs) in aquatic ecosystems. This chapter provides a comprehensive analysis of phosphorus metabolism in algae and cyanobacteria, highlighting the enzymatic pathways, genetic adaptations, and cellular mechanisms such as polyphosphate accumulation and alkaline phosphatase activity that allow bloom-forming species to thrive in phosphorus-rich or phosphorus-fluctuating environments. It explores the dual nature of phosphorus inputs external (e.g., agricultural runoff, urban waste) and internal (e.g., sediment release, biomass decomposition) in fueling bloom formation, persistence, and toxicity. The ecological and health impacts of phosphorus-induced blooms are examined in detail, including hypoxia, biodiversity loss, and the production of potent cyanotoxins. The chapter also discusses internal phosphorus cycling and microbial mediation in sediment–water interfaces, which contribute significantly to prolonged bloom events even after external sources are reduced. Effective management strategies are critically assessed, from best agricultural practices and constructed wetlands to cutting-edge approaches such as genetic engineering of algae and CRISPR-based biotechnological interventions. Finally, the chapter outlines key research needs, emphasizing the importance of understanding phosphorus–nitrogen interactions, microbial community functions, and the development of high-resolution monitoring and modeling tools. Bridging molecular mechanisms with ecosystem-level management, this chapter offers actionable insights into mitigating phosphorus-driven HABs and enhancing the resilience of aquatic ecosystems under increasing anthropogenic and climatic pressures.