Harmful algal blooms (HABs) are a global concern because they harm aquatic ecosystems and pose a risk to human health. Various physical, chemical, and biological approaches have been explored to control HABs. However, these methods have limitations in terms of cost, environmental impact, and effectiveness, particularly for large water bodies. Recently, the use of nanoparticles has emerged as a promising strategy for controlling HABs. Briefly, nanoparticles can act as anti-algae agents via several mechanisms, including photocatalysis, flocculation, oxidation, adsorption, and nutrient recovery. Compared with traditional methods, nanoparticle-based approaches offer advantages in terms of environmental friendliness, effectiveness, and specificity. However, the challenges and risks associated with nanoparticles, such as their toxicity and ecological impact, must be considered. In this review, we summarize recent research progress concerning the use of nanoparticles to control HABs, compare the advantages and disadvantages of different types of nanoparticles, discuss the factors influencing their effectiveness and environmental impact, and suggest future directions for research and development in this field. Additionally, we explore the causes of algal blooms, their harmful effects, and various treatment methods, including restricting eutrophication, biological control, and disrupting living conditions. The potential of photocatalysis for generating reactive oxygen species and nutrient control methods using nanomaterials are also discussed in detail. Moreover, the application of flocculants/coagulants for algal removal is highlighted, along with the challenges and potential solutions associated with their use. This comprehensive overview aims to contribute to the development of efficient and sustainable strategies for controlling HAB control.