This study investigates the response of dinoflagellate cysts to eutrophication and climatic anomalies in the Beibu Gulf over the past century using thtree sediment cores. Cyst assemblages were dominated by Protoperidinioid and Gonyaulacoid groups, and all cores recorded clear signals of terrigenous nutrient input. Results support that increased eutrophication raises total cyst abundance and autotrophic proportions, with the near-shore site showing a more pronounced response to anthropogenic nutrient loading, while the open-marine site exhibited stronger influence from human activities since 1978 and greater climatic modulation before that period. Climatic anomaly events, including ENSO, PDO, and monsoon variability, affected precipitation and runoff, thereby driving peaks and troughs in cyst abundance, although the intensity and timing of these responses were site-specific due to differences in location and regional circulation. In short, this study provides new sedimentological evidence for reconstructing long-term coastal environmental change in the Beibu Gulf and offers baseline data for integrating dinoflagellate cysts into ecological monitoring and rapid identification frameworks.