Coastal marine ecosystems face complex pressures from both anthropogenic activities and climate variability. However, due to the recent overwhelming signals of human-induced impacts, there is a paucity of evidence of paleoecological archives on the combined effects of anthropogenic and climatic impacts on coastal marine ecosystem. By analyzing ostracod(s) as an indicator of paleo benthic ecosystem at a unique, less urbanized marine site in Hong Kong, we discovered that moderate signal (i.e., not overly strong, like total defaunation) of gradual ostracod community shifts in response to mild human-induced stresses, and it gave us a chance to observe how the ecosystem change gradually in response to different types of human and climatic stressors. We found that pollutants shifted marine community from 1960s, aligning with Hong Kong's industrial development history. Local ecosystem has been affected by eutrophication gradually, starting rather late with major negative impacts from 1980s. We also found evidence of strong monsoons between similar to 1940s-1960s which aided the establishment of tropical species. Our integrated investigation on paleoecology, environmental human stresses (eutrophication, hypoxia, and pollution), climate change, and socioeconomics in the past century reveals complicated change of coastal marine ecosystem under various influences and provides a critical baseline for better optimized management and conservation in this rapidly developing subtropical region.