This study was based on the sediment quality triad (SQT) approach. The purpose was to define the extent and magnitude of contamination and biological effects associated with contaminants in the Massachusetts/Cape Cod Bays, Stellwagen Bank, and Boston Harbor. A stratified probabilistic sampling design was utilized to characterize the systems in terms of chemical contamination and benthic infaunal community structure. In addition, samples were taken in the vicinity of the new Boston sewage outfall in Massachusetts Bay and in Boston Harbor where the sewage outfall used to discharge. Toxicity bioassays were not done. A secondary objective was to coordinate with the NOAA NMFS to collect sediment and fish tissue samples at previously sampled Benthic Surveillance Program sites. This file contains sediment and water data measured in all areas sampled in 2004.