The Charles River Project provided an opportunity to simultaneously deploy a combination of biomonitoring techniques routinely used by the U.S. Geological Survey National Water Quality Assessment Program, the Biomonitoring of Environmental Status and Trends Project, and the Contaminant Biology Program at an urban site suspected to be contaminated with polycyclic aromatic hydrocarbons. In addition to these standardized methods, additional techniques were used to further elucidate contaminant exposure and potential impacts of exposure on biota. The purpose of the study was to generate a comprehensive, multi-metric data set to support assessment of contaminant exposure and effects at the site. Furthermore, the data set could be assessed to determine the relative performance of the standardized method suites typically used by the National Water Quality Assessment Program and the Biomonitoring of Environmental Status and Trends Project, as well as the additional biomonitoring methods used in the study to demonstrate ecological effects of contaminant exposure. The Contaminant Effects Workgroup, an advisory committee of the U.S. Geological Survey/Contaminant Biology Program, identified polycyclic aromatic hydrocarbons as the contaminant class of greatest concern in urban streams of all sizes. The reach of the Charles River near Watertown, Massachusetts, was selected as the site for this study based on the suspected presence of polycyclic aromatic hydrocarbon contamination and the presence of common carp (Cyprinus carpio), largemouth bass (Micropterus salmoides), and white sucker (Catostomus commersoni). All of these fish have extensive contaminant-exposure profiles related to polycyclic aromatic hydrocarbons and other environmental contaminants. This project represented a collaboration of universities, Department of the Interior bureaus including multiple components of the USGS (Biological Resources Discipline and Water Resources Discipline Science Centers, the Contaminant Biology Program, and the Status and Trends of Biological Resources Program), and the U.S. Fish and Wildlife Service. Samples for analyzing water chemistry, sediment chemistry and toxicity, fish community structure, tissue chemistry, and fish (20 carp, 20 bass, and 40 white sucker) and invertebrate pathology were collected in late August, 2005. This report provides results from the analyses of fish pathology, biomarkers of exposure and effects (reproductive, carcinogenic, genotoxic, and immunologic), sediment chemistry, toxicity, and fish and invertebrate community structure.