This comprehensive review explores the escalating challenge of nutrient enrichment in aquatic ecosystems, spotlighting the dire ecological threats posed by harmful algal blooms (HABs) and excessive particulate organic matter (POM). Investigating recent advancements in water treatment technologies and management strategies, the study emphasizes the critical need for a multifaceted approach that incorporates physical, chemical, and biological methods to effectively address these issues. By conducting detailed comparative analyses across diverse aquatic environments, it highlights the complexities of mitigating HABs and underscores the importance of environment-specific strategies. The paper advocates for sustainable, innovative solutions and international cooperation to enhance global water quality and ecosystem health. It calls for ongoing advancement, regular monitoring, and comprehensive research to adapt to emerging challenges, thus ensuring the preservation of aquatic biodiversity and the protection of communities reliant on these vital resources. The necessity of integrating technological innovation, ecological understanding, and global cooperation to safeguard aquatic ecosystems for future generations is paramount.