Long Island Sound (LIS) is a marginally marine urban estuary, with an east-west gradient in salinity and in indicators of contamination in the surface sediments (e.g., trace metals, the bacterial spore and sewage indicator Clostridium perfringens). Contaminants have higher concentrations in western Long Island, close to the main population center, where fine-grained sediments are focused. Since the 1970s, western LIS and to a lesser extent, central LIS, suffered summer hypoxia. We studied benthic foraminifera in 10 cores on depth transects in the main basins of LIS to document faunal changes since the time of European settlement. Sediment ages were determined using ¹³⁷Cs and ²¹⁰Pb data, in addition to historical metal pollution records. Before European settlement, the low-diversity benthic foraminiferal faunas were dominated by Elphidium excavatum (consuming living diatoms), while in the deeper regions Buccella frigida and Eggerella advena, using mainly dead organic matter, were common. In most cores, the absolute abundance of benthic foraminifera, as well as the relative abundance of E. excavatum, increased in the early-mid 1800s. The faunal changes coincided with an increase in trace metal concentration, and with human population growth in the region. The ecological changes may have been caused by increased productivity of diatoms, the main food of E. excavatum. Another period of major faunal changes started in western LIS after the late 1960s. Overall foraminiferal abundance decreased in several cores, but Ammonia beccarii, formerly absent at most locations, became common to dominant. Studies of grab samples taken from 1996 to 2001 document that the relative abundance of A. beccarii continued to increase during the late 1990s, even in the central basin. This increase in A. beccarii may be associated with the occurrence of hypoxia, possibly in conjunction with rising bottom water temperatures. On the other hand, high N/Si (resulting from increasing eutrophication) might favor primary producers other than diatoms (e.g., dinoflagelates), which would make E. excavatum less competitive. We thus document a coastal ecosystem that changed significantly with the enhanced nutrient input associated with human population growth in the middle 1800s, and again with more severe eutrophication over the last few decades.