The Chinese continental shelf, a region heavily influenced by human activities, has experienced significant ecological and environmental changes. Studying this area is of great scientific and practical importance for advancing oceanographic knowledge and promoting research on marine environmental protection and resource utilization. In recent years, intensified human activities have caused notable changes in the water environment, with Harmful Algal Blooms (HABs) showing new characteristics and shifts in dominant species. This paper provides a systematic review of research on water environmental changes and HABs occurrences in the Chinese continental shelf, offering a comprehensive analysis of major ecological and environmental challenges and outlining prospects for future research. The findings indicate that the marine ecological environment in this region is increasingly influenced by phosphorus limitation and the roles of organic nitrogen and phosphorus, accompanied by a shift in dominant HABs species from diatoms to dinoflagellates, and, in some areas, the simultaneous occurrence of HABs and green tides. These changes are driven by both ongoing alterations in terrestrial inputs and intrinsic self-regulatory mechanisms within the marine ecosystem, reflecting the cumulative effects of long-term environmental changes. Notably, there is a significant time lag between reductions in terrestrial pollution and decreases in HABs frequency, complicating the evaluation of management effectiveness and challenging the scientific determination of ecological risk thresholds or tipping points. Despite considerable progress in understanding the evolution of water environments and risks of HABs in China, significant challenges remain, including insufficient long-term and systematic observational data, the requirement to expand the research scope, and incomplete knowledge of land-sea interaction mechanisms. Future research should focus on elucidating land-sea coupling processes, enhancing marine environmental monitoring networks, improving data processing and technological innovation, and clarifying the thresholds for nitrogen and phosphorus management while developing integrated strategies that encompass monitoring, tracing, calculation, and management. These efforts are crucial for advancing marine environmental research in the Chinese continental shelf.