Sediments record the history of contamination to estuaries. Analysis of the concentrations of toxic organic compounds, contaminant and crustal metals, organic carbon content and isotopic composition in sediment cores from two estuarine systems in Buzzards Bay allowed reconstruction of human impacts over 350 years. Vertical distributions of the contaminants correlate with changes in the nature of watershed/estuarine activities. All contaminants were highly enriched (tens to hundreds times background) in modern New Bedford Harbor sediments. Enrichment began around the turn of the 20th century for all but PCBs, which were first synthesized in the 1930s. An increase in organic carbon content and a shift of carbon isotopes toward a more terrestrial signature illustrates increasing anthropogenic impact in New Bedford as population grew along with the industrial base. Institution of environmental protection measures in the late 20th century was reflected in decreased, although still substantially elevated, concentrations of contaminants. A lack of industrial development in Apponagansett Bay resulted in much lower concentrations of the same indicators, although specific contaminants related to the early whaling industry increased significantly above background as early as the late 18th century. The similarity of indicators in older portions of cores from NBH and unimpacted Apponagansett Bay demonstrates that cores can be used to establish reference conditions as successfully as using separate sites judged a priori to represent the reference state. The historical reconstruction approach provides the basis for establishing relationships between environmental stressors and factors that drive the stressors, as well as a framework for the assessment of ecological response(s) to environmental stressors over a range of time and/or exposure scales.