Advanced water treatment technologies have become increasingly critical in addressing global water quality challenges and ensuring sustainable water resource management. However, the ecological implications of these technologies, particularly their impact on planktonic communities, remain inadequately understood. This comprehensive review examines the effects of various advanced water treatment technologies—including membrane filtration, advanced oxidation processes, ultraviolet disinfection, ozonation, and nanotechnology-based treatments—on phytoplankton and zooplankton diversity in aquatic ecosystems. Through systematic analysis of peer-reviewed literature from 2015 to 2025, this study reveals that while these technologies effectively remove contaminants and pathogens, they simultaneously induce significant alterations in plankton community structure, species richness, and functional diversity. Membrane technologies demonstrate selective removal based on organism size, disproportionately affecting larger zooplankton species. Advanced oxidation processes and ozonation exhibit species-specific toxicity, with sensitive taxa experiencing population declines while tolerant species proliferate. The research identifies critical knowledge gaps regarding long-term ecological consequences, cascading effects on aquatic food webs, and the cumulative impacts of multiple treatment processes. This review emphasizes the necessity for integrated ecological assessments in water treatment facility design and operation, advocating for treatment optimization strategies that balance human health protection with ecosystem integrity preservation. The findings provide valuable insights for environmental engineers, water resource managers, and policymakers seeking to implement sustainable water treatment solutions that minimize adverse ecological impacts while maintaining treatment efficacy.