Dredging and remediation of contaminated Harbor sediments requires characterization of organic pollutants. In this paper, we apply a combination of Fourier transform IR attenuated total reflectance (FTIR-ATR) and synchrotron FTIR techniques to the investigation of sediments and related materials from New York/New Jersey Harbor and other locations. The FTIR techniques give information on the functional groups of the compounds found in the sediments and make possible measurements with a spatial resolution of about 0.015 mm. Comparisons of natural organic materials namely, river and groundwater humic substances, recent marine and lacustrine sediments, and ancient sedimentary kerogen show that contaminated NY/NJ Harbor sediments display a strong and distinct absorption in their IR spectra at 2850–2950 cm−1 identified as a CH stretching band, indicative of the presence of anthropogenic hydrocarbons. We suggest that the presence of this band could be used for rapid screening for the presence of contaminant organic compounds in sediments encountered in dredging operations and/or as an indicator for the efficacy of sediment decontamination technologies used for treatment of dredged material.