Soils and sediments contaminated with toxic organic and inorganic compounds harmful to the environment and to human health are common in the urban environment. We report here on aspects of a program being carried out in the New York/New Jersey Port region to develop methods for processing dredged material from the Port to make products that are safe for introduction to commercial markets. We discuss some of the results of the program in Computational Environmental Science, Laboratory Environmental Science, and Applied Environmental Science and indicate some possible directions for future work. Overall, the program elements integrate the scientific and engineering aspects with regulatory, commercial, urban planning, local governments, and community group interests. Well-developed connections between these components are critical to the ultimate success of efforts to cope with the problems caused by contaminated urban soils and sediments.