Benthic foraminifera are useful indicator species for monitoring environmental changes in near shore, environmentally stressed regions such as Long Island Sound (LIS), where severe anoxia/hypoxia was first observed in the early 1970s. We compared faunal and isotope data on benthic foraminifera collected in 1999 and 1996/1997 with (1) published records for the early 1960s (Buzas, 1965) and the late 1940s (Parker, 1952), and (2) faunal data collected in cores in western LIS at depths of 11 and 26m. In both cores, the number of foraminifera per gram of dry sediment increased dramatically at around 1850 AD. The sediment character changed at this point, and the abundance of benthic pellets increased, as did the number of molluscan shells per gram. The concentration of a sewage indicator, the bacterial spore Clostridium perfringens, increased and the foraminiferal assemblage changed. In both cores, the relative abundance of the herbivorous species Elphidium excavatum increased at about the same time as the foraminiferal abundance. We suggest that these changes around 150 years ago represent the initiation of anthropogenic eutrophication of LIS and of phytoplankton blooms, with increasing numbers of foraminifera as well as increasing relative abundance of a species that consumes fresh phytoplankton. More recent changes in the foraminiferal faunas started in the 1980s, when the relative abundance of Ammonia beccarii increased greatly in western LIS at depths of less than 15m. The species increased in relative abundance at depths greater than 25m only by the 1990s, at which time overall benthic foraminiferal abundances declined. We are not sure whether the increasing abundance of A. beccarii reflects increasing eutrophication and/or hypoxia, or whether increasing temperatures also play a role, but this recent change in faunal composition is unprecedented over the last few hundreds of years.