In this study, an offshoot of studies undertaken by the Washington State Department of Ecology (WDOE), the density and diversity of foraminiferal assemblages in Commencement and Elliott bays, two heavily industrialized embayments in Puget Sound, Washington (U.S.A) were compared and correlated with concentrations of metal pollutants and total polycyclic aromatic hydrocarbons (PAH). Samples used in this study were collected by the WDOE between 1998 and 2014, allowing comparison over a temporal range encompassing the beginnings of environmental remediation in both bays. The composition of the foraminiferal assemblages is typical of polluted estuaries globally, with the major taxa being Elphidiella hannai, Cribroelphidium excavatum, Bucella frigida and Eggerella advena. Foraminiferal density and diversity showed negative correlations with pollutants, however, these correlations were significant for only a few pollutants, and trends could not be attributed to any single one. Both embayments showed increasing diversity over time, and both had high proportions of calcareous tests that displayed signs of dissolution, indicating corrosive conditions in the water. In Elliott Bay the percentage of partially dissolved tests increased over time, suggesting remediation efforts have not been successful in all areas.