Results of both surface and core studies from two highly impacted estuaries (New Bedford Harbor, Massachusetts, USA and Halifax Harbour, Nova Scotia, Canada) are presented. New Bedford Harbor is in a highly industrialized area that has undergone severe degradation from a variety of sources for almost 400 years, and has been declared an EPA Superfund site. Halifax Harbour has been subjected mostly to domestic, rather than industrial, pollution since the founding of the city in 1749. Although many geochemical studies have been done in both estuaries, there are little baseline data on the biota. In this paper we use benthic foraminiferal assemblages retrieved from sediment cores to reconstruct the biotic changes of the recent past. It will then be possible to correlate faunal with already known geochemical changes. There are differences between these two sites both because New Bedford Harbor is shallower than Halifax Harbour and because of the different types of pollution. The character of the pollution has changed in New Bedford Harbor as remediation efforts are taking hold. This change can also be detected with the foraminifera. One interesting outcome is that deformities among one species of foraminifera, Haynesina orbiculare, appear to occur simultaneously with high PCBs 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.