The coastal bays of Delaware and Maryland are an important ecological and economic resource whose physical characteristics and location make them particularly vulnerable to the effects of pollutants. This project was undertaken as a collaborative effort between state and federal agencies to assess the ecological condition of this system and fill a data void identified in previous characterization studies. Two hundred sites were sampled in the summer of 1993 using a probability-based sampling design that was stratified to allow assessments of the coastal bays as a whole, each of four major subsystems within coastal bays (Rehoboth Bay, Indian River Bay, Assawoman Bay, and Chincoteague Bay) and four target areas of special interest to resource managers (upper Indian River, St. Martin River, Trappe Creek, and dead-end canals). Measures of biological response, sediment contaminants, and eutrophication were collected at each site using the same sampling methodologies and quality assurance/quality control procedures used by EPAs Environmental Monitoring and Assessment Program (EMAP). As an additional part of the study, trends in fish communities structure were assessed by collecting monthly beach seine and trawl measurements during the summer at about 70 sites where historic measurements of fish communities have been made.