Coastal environments are severely impacted by human activities, e.g., global warming due to greenhouse gas emissions and eutrophication with seasonal deoxygenation, due to nutrient input from fertilizers and sewage. Benthic foraminifera are a promising tool for assessment of ecological quality in coastal seas such as Long Island Sound (LIS: ‘The Urban Sea’), a shallow (mainly < 50 m deep) estuary in the eastern United States, established after the Younger Dryas (~11.5 ka). LIS has been affected by European settlement since the 1600s, with ecosystem disruption by the beaver fur-trade and deforestation. From the late 1800s, LIS was impacted by effects of population increase (New York City, Connecticut), further land-use changes and industrialization. Benthic foraminiferal assemblage, trace element and stable isotope data document that eutrophication and seasonal anoxia, combined with declining salinity due to fresh water rerouting in NY city, started in the mid 1800s. Low-diversity benthic assemblages, dominated by Elphidium species since LIS’ establishment, declined even more in diversity after the 1960s. In the 1990s, omnivorous Ammonia species increased in abundance relative to the kleptochloroplastic, diatom-using Elphidium in western LIS, possibly due to severe eutrophication leading to high N/Si, and declining diatom abundance. One would expect past episodes of global warming, such as the Paleocene-Eocene Thermal Maximum and other Eocene hyperthermals, to share patterns of environmental change with the present-future: global warming and eutrophication due to a more active hydrological cycle bringing in more nutrients, thus deoxygenation. Comparison of the effects of past and present-future global warming on coastal foraminiferal assemblages, however, is complicated because morphology of shelf regions in a Greenhouse world without polar ice sheets differed from that in the present, influenced by sea-level fluctuations of Pleistocene ice ages. In addition, todays' globally abundant, morphologically and genetically diverse, shallow-water genera Ammonia (low-mid latitude) and Elphidium (high-mid latitude) originated in the early Miocene and late Eocene, respectively, and early Eocene neritic benthic assemblages may have had a profoundly different population structure.