Both surface and core studies from two highly impacted estuaries (New Bedford Harbor, Massachusetts, USA and Halifax Harbour, Nova Scotia, Canada) were carried out to determine if benthic foraminifera could be used to detect changes through time in these areas. New Bedford Harbor is in a highly industrialized area that has undergone severe environmental stresses from a variety of sources for almost 400 years, and has been declared an U.S. Environmental Protection Agency (EPA) Superfund site (i.e., a site so impacted that a special EPA fund is set up to clean it up in designated time frame). Halifax Harbour has been subjected mostly to domestic pollution (i.e., organic carbon produced by human wastes), rather than industrial (chemical) pollution since the founding of the city in 1749. Although many geochemical studies have been done in both estuaries, there are few baseline data on the biota. In this paper we use benthic foraminiferal assemblages retrieved from sediment cores to reconstruct biotic changes of the recent past. It is then possible to correlate faunal changes with already known geochemical parameters. The character of the pollution has changed in New Bedford Harbor as remediation efforts have taken hold. This change was detected with the foraminifera. One outcome is that deformities among one species, Haynesina orbiculare, appear to occur simultaneously with high polychlorinated biphenyls (PCB’s) in the sediments. In Halifax Harbour, where the largest impact is due to high organic input from domestic sources, species tolerant of low-oxygen conditions are most prominent at present. Core studies show that prior to the rapid growth of Halifax (in the 1960s) the organic input was much lower than at present. The higher input of organic carbon (OC) at present is indicated by foraminiferal species tolerant of high OC in cores since 1960, generally those with agglutinated as opposed to calcareous tests. We define industrial vs. OC pollution in sediments using foraminifera as proxies, and further, the environmental history is accurately depicted without original baseline data. Data from these two estuaries can be compared to other sites where degradation may be in different stages, which can be assessed by looking at foraminiferal faunas in those areas.