The Raritan River drains a highly urbanized and industrialized area of New Jersey. Extensive areas of this waterway receive finegrained sediments from within the drainage basin and from Raritan Bay, which are believed to be contaminated with pollutants. The transition from fluvial to estuarine conditions and seaward enlargement of the estuary due to increasing volume of tidal discharges result in a distinctive sequence of downstream changes in channel morphology, processes, and sedimentary environments. These are mapped and are classified as transport zones (above the head of tide), temporary storage areas (upper and middle estuaries), and permanent sinks (mud benches, dredged areas, tidal marshes) for fine sediments. These designations can be used for more cost-effective sampling, that is, “focused sampling” of sediments likely to contain pollutants. A sediment budget for the estuary indicates it is a sediment sink, with the largest input coming from landward sources. This analysis can serve as a guide to assessment and management of contaminated environments.