With the renovation of Boston Harbor's Deer Island wastewater treatment plant and the extension of its diffuser pipes 15km further into Massachusetts Bay, there arose the question whether the increased load of its secondary-treated wastewater contained significant amounts of phenolic endocrine disrupting chemicals (EDCs). Sampling from an oceanographic research vessel during the summers of 2003 and 2004 allowed for a unique opportunity to obtain clam, zooplankton, and bottom sediment samples. The samples were prepared by enhanced organic-solvent microwave digestion, followed by solid-phase extraction (SPE), derivatization and then analyzed by gas chromatography–mass spectrometry (GC–MS) or left un-derivatized and analyzed by LC–UV and liquid chromatography–mass spectrometry (LC–MS). The marine samples, especially parts of the clams, zooplankton and certain bottom sediments were found to contain primarily bisphenol A (BPA) at concentrations of 1–30ng/g.